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October 26, 2017 18:11
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cnvkit segmentation fault
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| ##fileformat=VCFv4.2 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample"> | |
| ##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor"> | |
| ##FILTER=<ID=clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads"> | |
| ##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic"> | |
| ##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor"> | |
| ##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal"> | |
| ##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals"> | |
| ##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region"> | |
| ##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only"> | |
| ##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold"> | |
| ##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD"> | |
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| ##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> | |
| ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> | |
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | |
| ##GATKCommandLine.MuTect2=<ID=MuTect2,Version=3.8-0-ge9d806836,Date="Wed Oct 11 00:43:45 CEST 2017",Epoch=1507675425618,CommandLineOptions="analysis_type=MuTect2 input_file=[/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bamprep/P00132893_tumor/chr1/P00132893_tumor-sort-recal-chr1_0_15687266-prep.bam, /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bamprep/P00132893_normal/chr1/P00132893_normal-sort-recal-chr1_0_15687266-prep.bam] showFullBamList=false read_buffer_size=null read_filter=[BadCigar, NotPrimaryAlignment] disable_read_filter=[] intervals=[/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/chr1/1-chr1_0_15687266-regions-nolcr.bed] excludeIntervals=null interval_set_rule=INTERSECTION interval_merging=ALL interval_padding=0 reference_sequence=/mnt/home_nfs1/mbeyens/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=LENIENT_VCF_PROCESSING use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false cosmic=[] normal_panel=[] dbsnp=(RodBinding name= source=UNBOUND) m2debug=false artifact_detection_mode=false initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=6.3 normal_lod=2.2 dbsnp_normal_lod=5.5 max_alt_alleles_in_normal_count=1 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 enable_strand_artifact_filter=false enable_clustered_read_position_filter=false pir_median_threshold=10.0 pir_mad_threshold=3.0 debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false debug_read_name=null MQ_filtering_level=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, FisherStrand, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, ReadPosRankSumTest, RMSMappingQuality, GCContent, HaplotypeScore, HomopolymerRun, DepthPerAlleleBySample, Coverage] excludeAnnotation=[SpanningDeletions] out=(Stream) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 keepRG=null min_base_quality_score=10 errorCorrectReads=false captureAssemblyFailureBAM=false dontUseSoftClippedBases=false justDetermineActiveRegions=false doNotRunPhysicalPhasing=false maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> | |
| ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | |
| ##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype"> | |
| ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | |
| ##INFO=<ID=GC,Number=1,Type=Float,Description="GC content around the variant (see docs for window size details)"> | |
| ##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant"> | |
| ##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"> | |
| ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> | |
| ##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region"> | |
| ##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region"> | |
| ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> | |
| ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> | |
| ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | |
| ##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score"> | |
| ##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals"> | |
| ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | |
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | |
| ##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score"> | |
| ##SAMPLE=<ID=NORMAL,SampleName=P00132893_normal,File=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bamprep/P00132893_normal/chr1/P00132893_normal-sort-recal-chr1_0_15687266-prep.bam> | |
| ##SAMPLE=<ID=TUMOR,SampleName=P00132893_tumor,File=/mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bamprep/P00132893_tumor/chr1/P00132893_tumor-sort-recal-chr1_0_15687266-prep.bam> | |
| ##contig=<ID=chrM,length=16571,assembly=hg19> | |
| ##contig=<ID=chr1,length=249250621,assembly=hg19> | |
| ##contig=<ID=chr2,length=243199373,assembly=hg19> | |
| ##contig=<ID=chr3,length=198022430,assembly=hg19> | |
| ##contig=<ID=chr4,length=191154276,assembly=hg19> | |
| ##contig=<ID=chr5,length=180915260,assembly=hg19> | |
| ##contig=<ID=chr6,length=171115067,assembly=hg19> | |
| ##contig=<ID=chr7,length=159138663,assembly=hg19> | |
| ##contig=<ID=chr8,length=146364022,assembly=hg19> | |
| ##contig=<ID=chr9,length=141213431,assembly=hg19> | |
| ##contig=<ID=chr10,length=135534747,assembly=hg19> | |
| ##contig=<ID=chr11,length=135006516,assembly=hg19> | |
| ##contig=<ID=chr12,length=133851895,assembly=hg19> | |
| ##contig=<ID=chr13,length=115169878,assembly=hg19> | |
| ##contig=<ID=chr14,length=107349540,assembly=hg19> | |
| ##contig=<ID=chr15,length=102531392,assembly=hg19> | |
| ##contig=<ID=chr16,length=90354753,assembly=hg19> | |
| ##contig=<ID=chr17,length=81195210,assembly=hg19> | |
| ##contig=<ID=chr18,length=78077248,assembly=hg19> | |
| ##contig=<ID=chr19,length=59128983,assembly=hg19> | |
| ##contig=<ID=chr20,length=63025520,assembly=hg19> | |
| ##contig=<ID=chr21,length=48129895,assembly=hg19> | |
| ##contig=<ID=chr22,length=51304566,assembly=hg19> | |
| ##contig=<ID=chrX,length=155270560,assembly=hg19> | |
| ##contig=<ID=chrY,length=59373566,assembly=hg19> | |
| ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19> | |
| ##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19> | |
| ##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19> | |
| ##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19> | |
| ##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19> | |
| ##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19> | |
| ##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19> | |
| ##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19> | |
| ##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19> | |
| ##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19> | |
| ##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19> | |
| ##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19> | |
| ##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19> | |
| ##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19> | |
| ##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19> | |
| ##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19> | |
| ##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19> | |
| ##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19> | |
| ##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19> | |
| ##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19> | |
| ##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19> | |
| ##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19> | |
| ##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19> | |
| ##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19> | |
| ##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19> | |
| ##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19> | |
| ##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19> | |
| ##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19> | |
| ##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19> | |
| ##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19> | |
| ##reference=file:///mnt/home_nfs1/mbeyens/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa | |
| ##bcftools_concatVersion=1.6+htslib-1.6 | |
| ##bcftools_concatCommand=concat --allow-overlaps -O z --file-list /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-files.list -o /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/bcbiotx/tmpEcajo8/1.vcf.gz; Date=Thu Oct 12 22:19:20 2017 | |
| ##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani" | |
| ##SnpEffCmd="SnpEff -cancer -i vcf -o vcf -csvStats /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-stats.csv -s /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1-effects-stats.html GRCh37.75 /mnt/home_nfs1/shared_data_core/PNET/10PNET_FF_gitta/raw_data/paired_analysis/work/mutect2/1.vcf.gz " | |
| ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> | |
| ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> | |
| ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> | |
| ##SAMPLE=<ID=P00132893_tumor,Genomes=Tumor> | |
| ##SAMPLE=<ID=P00132893_normal,Genomes=Germline> | |
| ##PEDIGREE=<Derived=P00132893_tumor,Original=P00132893_normal> | |
| ##bcftools_viewVersion=1.6+htslib-1.6 | |
| ##bcftools_viewCommand=view; Date=Thu Oct 12 22:22:15 2017 | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT P00132893_tumor P00132893_normal | |
| chr1 14522 . G A . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=126;ECNT=3;FS=11.648;HCNT=5;MAX_ED=68;MIN_ED=20;MQ=39.63;MQ0=31;MQRankSum=-2.823;NLOD=8.43;ReadPosRankSum=-0.296;TLOD=7.37;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*113G>A|||||113|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*110G>A|||||110|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*113G>A|||||113|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*852G>A|||||852|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1254-21C>T||||||,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1492-20C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|12/12|n.1624C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|9/9|n.1257C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|10/10|n.1510C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:46,3:0.071:49:0|1:14522_G_A 0/0:40,0:0:40:0|1:14522_G_A | |
| chr1 14542 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=129;ECNT=3;FS=19.059;HCNT=5;MAX_ED=68;MIN_ED=20;MQ=41.37;MQ0=26;MQRankSum=-2.534;NLOD=2.58;ReadPosRankSum=-1.247;TLOD=10.78;ANN=G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*133A>G|||||133|,G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*130A>G|||||130|,G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*133A>G|||||133|,G|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*872A>G|||||872|,G|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1254-41T>C||||||,G|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1492-40T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|12/12|n.1604T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|9/9|n.1237T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|10/10|n.1490T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:44,5:0.111:49:0|1:14522_G_A 0/0:46,2:0.05:48:0|1:14522_G_A | |
| chr1 14590 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=157;ECNT=3;FS=16.281;HCNT=3;MAX_ED=68;MIN_ED=20;MQ=43.07;MQ0=24;MQRankSum=-2.991;NLOD=8.66;ReadPosRankSum=0.135;TLOD=7.98;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*181G>A|||||181|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*178G>A|||||178|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*181G>A|||||181|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*920G>A|||||920|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1254-89C>T||||||,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1492-88C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|12/12|n.1556C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|9/9|n.1189C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|10/10|n.1442C>T|||||| GT:AD:AF:DP 0/1:64,6:0.098:70 0/0:54,2:0.042:56 | |
| chr1 14792 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=505;ECNT=2;FS=0;HCNT=4;MAX_ED=23;MIN_ED=23;MQ=41.84;MQ0=44;MQRankSum=2.138;NLOD=12.74;ReadPosRankSum=0.873;TLOD=5.65;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*383G>A|||||383|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*380G>A|||||380|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*383G>A|||||383|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*1122G>A|||||1122|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1253+213C>T||||||,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1491+208C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|12/12|n.1354C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|9/9|n.987C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|10/10|n.1240C>T|||||| GT:AD:AF:DP 0/1:281,8:0.02:289 0/0:111,10:0.058:121 | |
| chr1 14815 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=537;ECNT=2;FS=0;HCNT=4;MAX_ED=23;MIN_ED=23;MQ=44.03;MQ0=45;MQRankSum=-4.015;NLOD=23.90;ReadPosRankSum=2.634;TLOD=10.76;ANN=T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*406C>T|||||406|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*403C>T|||||403|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*406C>T|||||406|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*1145C>T|||||1145|,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1253+190G>A||||||,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1491+185G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|12/12|n.1331G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|9/9|n.964G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|10/10|n.1217G>A|||||| GT:AD:AF:DP 0/1:299,16:0.036:315 0/0:128,2:0.011:130 | |
| chr1 14932 . G T . PASS ClippingRankSum=0;DP=553;ECNT=1;FS=12.903;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=51.9;MQ0=13;MQRankSum=-1.315;NLOD=28.00;ReadPosRankSum=-2.192;TLOD=7.64;ANN=T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*523G>T|||||523|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*520G>T|||||520|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*523G>T|||||523|,T|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*1262G>T|||||1262|,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|11/11|n.1316+38C>A||||||,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|8/8|n.949+38C>A||||||,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|9/9|n.1202+38C>A||||||,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|10/10|n.1253+73C>A||||||,T|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|12/12|n.1491+68C>A|||||| GT:AD:AF:DP 0/1:350,6:0.02:356 0/0:164,6:0.049:170 | |
| chr1 16949 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1224;ECNT=4;FS=16.573;HCNT=20;MAX_ED=47;MIN_ED=14;MQ=31.41;MQ0=749;MQRankSum=-1.694;NLOD=11.57;ReadPosRankSum=-1.235;TLOD=7.95;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*2540A>C|||||2540|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*2537A>C|||||2537|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*2540A>C|||||2540|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*3279A>C|||||3279|,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|7/12|n.843T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/9|n.785T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|6/10|n.731T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|7/11|n.817T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|7/13|n.1054T>G|||||| GT:AD:AF:DP 0/1:137,8:0.059:145 0/0:296,13:0.055:309 | |
| chr1 16963 . G A . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1304;ECNT=4;FS=22.891;HCNT=9;MAX_ED=47;MIN_ED=14;MQ=31.33;MQ0=831;MQRankSum=4.26;NLOD=2.07;ReadPosRankSum=0.109;TLOD=4.54;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*2554G>A|||||2554|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*2551G>A|||||2551|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*2554G>A|||||2554|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*3293G>A|||||3293|,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|7/12|n.829C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/9|n.771C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|6/10|n.717C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|7/11|n.803C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|7/13|n.1040C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:123,2:0.016:125:0|1:16963_G_A 0/0:273,56:0.174:329:0|1:16963_G_A | |
| chr1 16975 . G A . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1304;ECNT=4;FS=15.081;HCNT=9;MAX_ED=47;MIN_ED=14;MQ=31.07;MQ0=850;MQRankSum=3.61;NLOD=1.77;ReadPosRankSum=1.622;TLOD=4.65;ANN=A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*2566G>A|||||2566|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*2563G>A|||||2563|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*2566G>A|||||2566|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*3305G>A|||||3305|,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|7/12|n.817C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/9|n.759C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|6/10|n.705C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|7/11|n.791C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|7/13|n.1028C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:103,2:0.018:105:0|1:16963_G_A 0/0:275,51:0.174:326:0|1:16963_G_A | |
| chr1 16996 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1290;ECNT=4;FS=29.717;HCNT=14;MAX_ED=47;MIN_ED=14;MQ=30.64;MQ0=872;MQRankSum=-0.647;NLOD=2.01;ReadPosRankSum=0.689;TLOD=10.09;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*2587T>C|||||2587|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*2584T>C|||||2584|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*2587T>C|||||2587|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*3326T>C|||||3326|,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|7/12|n.796A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/9|n.738A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|6/10|n.684A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|7/11|n.770A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|7/13|n.1007A>G|||||| GT:AD:AF:DP 0/1:73,8:0.098:81 0/0:291,30:0.11:321 | |
| chr1 137563 . T C . germline_risk ClippingRankSum=0;DP=489;ECNT=1;FS=2.861;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=30.18;MQ0=314;MQRankSum=-0.076;NLOD=0.506;ReadPosRankSum=1.025;TLOD=8.09;ANN=C|upstream_gene_variant|MODIFIER|RP11-34P13.15|ENSG00000268903|transcript|ENST00000494149|processed_pseudogene||n.-1668A>G|||||1668|,C|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|transcript|ENST00000453576|lincRNA||n.-3997A>G|||||3997|,C|downstream_gene_variant|MODIFIER|CICP27|ENSG00000233750|transcript|ENST00000442987|processed_pseudogene||n.*2727T>C|||||2727|,C|downstream_gene_variant|MODIFIER|RP11-34P13.16|ENSG00000269981|transcript|ENST00000595919|processed_pseudogene||n.*119A>G|||||119|,C|downstream_gene_variant|MODIFIER|RP11-34P13.14|ENSG00000239906|transcript|ENST00000493797|antisense||n.*2227A>G|||||2227|,C|downstream_gene_variant|MODIFIER|RP11-34P13.13|ENSG00000241860|transcript|ENST00000484859|antisense||n.*3911A>G|||||3911|,C|intron_variant|MODIFIER|AL627309.1|ENSG00000237683|transcript|ENST00000423372|protein_coding|1/1|c.*909+58A>G||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:29,6:0.217:35 0/0:96,21:0.193:117 | |
| chr1 762330 . G T . clustered_events ClippingRankSum=0;DP=214;ECNT=2;FS=5.064;HCNT=1;MAX_ED=15;MIN_ED=15;MQ=47.13;MQ0=19;MQRankSum=-2.471;NLOD=13.54;ReadPosRankSum=-2.454;TLOD=7.64;ANN=T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000445118|lincRNA||n.-658G>T|||||658|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000610067|lincRNA||n.-711G>T|||||711|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000441765|lincRNA||n.-717G>T|||||717|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000609139|lincRNA||n.-719G>T|||||719|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000449005|lincRNA||n.-723G>T|||||723|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000416570|lincRNA||n.-749G>T|||||749|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000448975|lincRNA||n.-749G>T|||||749|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000608189|lincRNA||n.-2113G>T|||||2113|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000609009|lincRNA||n.-2113G>T|||||2113|,T|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000415295|lincRNA||n.-4655G>T|||||4655|,T|non_coding_transcript_exon_variant|MODIFIER|LINC00115|ENSG00000225880|transcript|ENST00000473798|lincRNA|1/1|n.573C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC00115|ENSG00000225880|transcript|ENST00000536430|lincRNA|1/1|n.557C>A|||||| GT:AD:AF:DP:PGT:PID 0/1:121,4:0.03:125:0|1:762330_G_T 0/0:65,0:0:65:0|1:762330_G_T | |
| chr1 762345 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=202;ECNT=2;FS=8.516;HCNT=1;MAX_ED=15;MIN_ED=15;MQ=45.5;MQ0=19;MQRankSum=-1.338;NLOD=9.47;ReadPosRankSum=-2.492;TLOD=8.21;ANN=G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000445118|lincRNA||n.-643A>G|||||643|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000610067|lincRNA||n.-696A>G|||||696|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000441765|lincRNA||n.-702A>G|||||702|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000609139|lincRNA||n.-704A>G|||||704|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000449005|lincRNA||n.-708A>G|||||708|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000416570|lincRNA||n.-734A>G|||||734|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000448975|lincRNA||n.-734A>G|||||734|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000608189|lincRNA||n.-2098A>G|||||2098|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000609009|lincRNA||n.-2098A>G|||||2098|,G|upstream_gene_variant|MODIFIER|LINC01128|ENSG00000228794|transcript|ENST00000415295|lincRNA||n.-4640A>G|||||4640|,G|non_coding_transcript_exon_variant|MODIFIER|LINC00115|ENSG00000225880|transcript|ENST00000473798|lincRNA|1/1|n.558T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|LINC00115|ENSG00000225880|transcript|ENST00000536430|lincRNA|1/1|n.542T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:113,6:0.043:119:0|1:762330_G_T 0/0:57,1:0.023:58:0|1:762330_G_T | |
| chr1 906272 . A C . germline_risk;t_lod_fstar ClippingRankSum=0;DP=7;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.902;ReadPosRankSum=1.668;TLOD=5.92;ANN=C|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|transcript|ENST00000379409|protein_coding|5/15|c.618A>C|p.Ala206Ala|648/2455|618/1992|206/663||,C|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|transcript|ENST00000379410|protein_coding|6/16|c.498A>C|p.Ala166Ala|533/2404|498/1836|166/611||,C|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|transcript|ENST00000379407|protein_coding|6/15|c.498A>C|p.Ala166Ala|528/2194|498/1731|166/576||,C|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000491024|protein_coding||c.-2620A>C|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000433179|protein_coding||c.*5280T>G|||||4307|,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000341290|protein_coding||c.*5280T>G|||||4312|,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000479361|retained_intron||n.*4313T>G|||||4313|,C|non_coding_transcript_exon_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000480267|retained_intron|1/3|n.18A>C|||||| GT:AD:AF:DP 0/1:1,2:0.667:3 0/0:4,0:0:4 | |
| chr1 906683 . A ACCCCCCC . clustered_events;germline_risk;t_lod_fstar ClippingRankSum=0;DP=20;ECNT=2;FS=8.113;HCNT=1;MAX_ED=5;MIN_ED=5;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.51;ReadPosRankSum=-1.494;TLOD=4.48;ANN=ACCCCCCC|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000491024|protein_coding||c.-2209_-2208insCCCCCCC|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,ACCCCCCC|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000433179|protein_coding||c.*4868_*4869insGGGGGGG|||||3895|,ACCCCCCC|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000341290|protein_coding||c.*4868_*4869insGGGGGGG|||||3900|,ACCCCCCC|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000479361|retained_intron||n.*3901_*3902insGGGGGGG|||||3901|,ACCCCCCC|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379409|protein_coding|6/14|c.865-17_865-16insCCCCCCC||||||INFO_REALIGN_3_PRIME,ACCCCCCC|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379410|protein_coding|7/15|c.709-17_709-16insCCCCCCC||||||INFO_REALIGN_3_PRIME,ACCCCCCC|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379407|protein_coding|7/14|c.745-17_745-16insCCCCCCC||||||INFO_REALIGN_3_PRIME,ACCCCCCC|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000480267|retained_intron|2/2|n.265-17_265-16insCCCCCCC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:10,5:0.125:15 0/0:5,0:0:5 | |
| chr1 906688 . A C . clustered_events;germline_risk;t_lod_fstar ClippingRankSum=0;DP=19;ECNT=2;FS=12.381;HCNT=2;MAX_ED=5;MIN_ED=5;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.81;ReadPosRankSum=-1.287;TLOD=4.90;ANN=C|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000491024|protein_coding||c.-2204A>C|||||2204|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000433179|protein_coding||c.*4864T>G|||||3891|,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000341290|protein_coding||c.*4864T>G|||||3896|,C|downstream_gene_variant|MODIFIER|C1orf170|ENSG00000187642|transcript|ENST00000479361|retained_intron||n.*3897T>G|||||3897|,C|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379409|protein_coding|6/14|c.865-16A>C||||||,C|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379410|protein_coding|7/15|c.709-16A>C||||||,C|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379407|protein_coding|7/14|c.745-16A>C||||||,C|intron_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000480267|retained_intron|2/2|n.265-16A>C|||||| GT:AD:AF:DP 0/1:10,3:0.182:13 0/0:6,0:0:6 | |
| chr1 980898 . G T . t_lod_fstar ClippingRankSum=0;DP=59;ECNT=1;FS=2.045;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=0.245;TLOD=4.04;ANN=T|missense_variant|MODERATE|AGRN|ENSG00000188157|transcript|ENST00000379370|protein_coding|14/36|c.2531G>T|p.Cys844Phe|2581/7323|2531/6138|844/2045||,T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000466223|retained_intron||n.-1683G>T|||||1683|,T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000478677|retained_intron||n.-1957G>T|||||1957|,T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000492947|retained_intron||n.-3011G>T|||||3011|,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000477585|processed_transcript||n.*4793G>T|||||4793|,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000469403|retained_intron||n.*4121G>T|||||4121|,T|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|transcript|ENST00000479707|retained_intron|1/4|n.120G>T|||||| GT:AD:AF:DP 0/1:39,4:0.065:43 0/0:16,0:0:16 | |
| chr1 1572750 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=167;ECNT=2;FS=26.348;HCNT=10;MAX_ED=4;MIN_ED=4;MQ=58.15;MQ0=3;MQRankSum=-11.226;NLOD=3.64;ReadPosRankSum=-2.564;TLOD=26.68;ANN=A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000356026|protein_coding||c.*2749C>A|||||2720|,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000472264|protein_coding||c.*4251C>A|||||4251|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000512731|nonsense_mediated_decay||c.*3894C>A|||||2900|,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000378675|protein_coding||c.*2828C>A|||||2720|,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000479814|protein_coding||c.*2828C>A|||||2723|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000435358|protein_coding||c.*2828C>A|||||2806|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000503792|protein_coding||c.*2828C>A|||||2806|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000489782|retained_intron||n.*2770C>A|||||2770|,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000486400|retained_intron||n.*2766C>A|||||2766|,A|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000490017|nonsense_mediated_decay||c.*2749C>A|||||2111|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000407249|protein_coding|15/20|c.1579+20G>T||||||,A|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000513088|protein_coding|9/14|c.1075+20G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000341832|protein_coding|14/19|c.1438+20G>T||||||,A|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000317673|protein_coding|15/20|c.1573+20G>T||||||,A|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000340677|protein_coding|14/19|c.1540+20G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:97,8:0.106:105:0|1:1572750_C_A 0/0:54,2:0.048:56:0|1:1572750_C_A | |
| chr1 1572754 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=170;ECNT=2;FS=31.952;HCNT=10;MAX_ED=4;MIN_ED=4;MQ=57.79;MQ0=3;MQRankSum=-11.046;NLOD=3.64;ReadPosRankSum=-2.473;TLOD=28.99;ANN=C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000356026|protein_coding||c.*2753T>C|||||2724|,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000472264|protein_coding||c.*4255T>C|||||4255|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000512731|nonsense_mediated_decay||c.*3898T>C|||||2904|,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000378675|protein_coding||c.*2832T>C|||||2724|,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000479814|protein_coding||c.*2832T>C|||||2727|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000435358|protein_coding||c.*2832T>C|||||2810|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000503792|protein_coding||c.*2832T>C|||||2810|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000489782|retained_intron||n.*2774T>C|||||2774|,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000486400|retained_intron||n.*2770T>C|||||2770|,C|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000490017|nonsense_mediated_decay||c.*2753T>C|||||2115|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000407249|protein_coding|15/20|c.1579+16A>G||||||,C|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000513088|protein_coding|9/14|c.1075+16A>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000341832|protein_coding|14/19|c.1438+16A>G||||||,C|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000317673|protein_coding|15/20|c.1573+16A>G||||||,C|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000340677|protein_coding|14/19|c.1540+16A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:98,10:0.118:108:0|1:1572750_C_A 0/0:54,2:0.048:56:0|1:1572750_C_A | |
| chr1 1573078 . A G . t_lod_fstar ClippingRankSum=0;DP=139;ECNT=1;FS=17.404;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=59.76;MQ0=0;MQRankSum=-6.682;NLOD=4.84;ReadPosRankSum=-1.692;TLOD=5.07;ANN=G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000356026|protein_coding||c.*3077A>G|||||3048|,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000472264|protein_coding||c.*4579A>G|||||4579|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000512731|nonsense_mediated_decay||c.*4222A>G|||||3228|,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000378675|protein_coding||c.*3156A>G|||||3048|,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000479814|protein_coding||c.*3156A>G|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000435358|protein_coding||c.*3156A>G|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000503792|protein_coding||c.*3156A>G|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000489782|retained_intron||n.*3098A>G|||||3098|,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000486400|retained_intron||n.*3094A>G|||||3094|,G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST00000490017|nonsense_mediated_decay||c.*3077A>G|||||2439|WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000407249|protein_coding|14/20|c.1473+46T>C||||||,G|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000513088|protein_coding|8/14|c.969+46T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000341832|protein_coding|13/19|c.1332+46T>C||||||,G|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000317673|protein_coding|14/20|c.1467+46T>C||||||,G|intron_variant|MODIFIER|CDK11B|ENSG00000248333|transcript|ENST00000340677|protein_coding|13/19|c.1434+46T>C|||||| GT:AD:AF:DP 0/1:86,2:0.029:88 0/0:49,2:0.043:51 | |
| chr1 1666303 . T C . PASS ClippingRankSum=0;DP=461;ECNT=1;FS=68.035;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=48.26;MQ0=31;MQRankSum=-1.713;NLOD=16.77;ReadPosRankSum=-3.981;TLOD=19.48;ANN=C|upstream_gene_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000418950|transcribed_processed_pseudogene||n.-953T>C|||||953|,C|downstream_gene_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000417099|processed_transcript||n.*2960T>C|||||2960|,C|intron_variant|MODIFIER|RP1-283E3.8|ENSG00000268575|transcript|ENST00000598846|processed_transcript|1/19|n.2486-29A>G||||||,C|intron_variant|MODIFIER|SLC35E2|ENSG00000215790|transcript|ENST00000246421|protein_coding|4/5|c.587-29A>G||||||,C|intron_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000577672|processed_transcript|1/1|n.253-953T>C||||||,C|intron_variant|MODIFIER|SLC35E2|ENSG00000215790|transcript|ENST00000355439|protein_coding|5/6|c.587-29A>G||||||,C|intron_variant|MODIFIER|SLC35E2|ENSG00000215790|transcript|ENST00000400924|protein_coding|4/5|c.587-29A>G||||||,C|intron_variant|MODIFIER|SLC35E2|ENSG00000215790|transcript|ENST00000475229|processed_transcript|1/2|n.72-29A>G||||||,C|intron_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000424604|processed_transcript|1/1|n.292-953T>C|||||| GT:AD:AF:DP 0/1:191,14:0.091:205 0/0:166,17:0.114:183 | |
| chr1 1670432 . T C . germline_risk ClippingRankSum=0;DP=312;ECNT=1;FS=90.486;HCNT=34;MAX_ED=.;MIN_ED=.;MQ=47.66;MQ0=2;MQRankSum=0.112;NLOD=1.37;ReadPosRankSum=-1.399;TLOD=20.01;ANN=C|synonymous_variant|LOW|SLC35E2|ENSG00000215790|transcript|ENST00000246421|protein_coding|3/6|c.387A>G|p.Leu129Leu|803/1430|387/801|129/266||,C|synonymous_variant|LOW|SLC35E2|ENSG00000215790|transcript|ENST00000355439|protein_coding|4/7|c.387A>G|p.Leu129Leu|1148/2078|387/741|129/246||,C|synonymous_variant|LOW|SLC35E2|ENSG00000215790|transcript|ENST00000400924|protein_coding|3/6|c.387A>G|p.Leu129Leu|803/1157|387/741|129/246||,C|upstream_gene_variant|MODIFIER|RP1-283E3.8|ENSG00000268575|transcript|ENST00000598846|processed_transcript||n.-1305A>G|||||1305|,C|upstream_gene_variant|MODIFIER|SLC35E2|ENSG00000215790|transcript|ENST00000475229|processed_transcript||n.-3719A>G|||||3719|,C|downstream_gene_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000577672|processed_transcript||n.*3020T>C|||||3020|,C|downstream_gene_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000424604|processed_transcript||n.*3018T>C|||||3018|,C|downstream_gene_variant|MODIFIER|RP1-283E3.4|ENSG00000227775|transcript|ENST00000418950|transcribed_processed_pseudogene||n.*1742T>C|||||1742| GT:AD:AF:DP 0/1:173,12:0.085:185 0/0:105,11:0.104:116 | |
| chr1 4772582 . GCCA G . t_lod_fstar ClippingRankSum=0;DP=153;ECNT=1;FS=4.017;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.63;ReadPosRankSum=0.599;TLOD=6.06;ANN=G|disruptive_inframe_deletion|MODERATE|AJAP1|ENSG00000196581|transcript|ENST00000378190|protein_coding|2/6|c.672_674delCAC|p.Thr225del|1366/2383|672/1236|224/411||INFO_REALIGN_3_PRIME,G|disruptive_inframe_deletion|MODERATE|AJAP1|ENSG00000196581|transcript|ENST00000378191|protein_coding|2/6|c.672_674delCAC|p.Thr225del|1053/11666|672/1236|224/411||INFO_REALIGN_3_PRIME,G|downstream_gene_variant|MODIFIER|AJAP1|ENSG00000196581|transcript|ENST00000466761|processed_transcript||n.*358_*360delCCA|||||358| GT:AD:AF:DP 0/1:77,6:0.067:83 0/0:47,0:0:47 | |
| chr1 6649015 . G T . t_lod_fstar ClippingRankSum=0;DP=128;ECNT=1;FS=10.698;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.43;ReadPosRankSum=0.744;TLOD=5.13;ANN=T|stop_gained|HIGH|ZBTB48|ENSG00000204859|transcript|ENST00000377674|protein_coding|11/11|c.1810G>T|p.Glu604*|1968/2293|1810/2067|604/688||,T|3_prime_UTR_variant|MODIFIER|ZBTB48|ENSG00000204859|transcript|ENST00000466813|nonsense_mediated_decay|6/6|c.*198G>T|||||582|,T|downstream_gene_variant|MODIFIER|KLHL21|ENSG00000162413|transcript|ENST00000377658|protein_coding||c.*4410C>A|||||1769|,T|downstream_gene_variant|MODIFIER|ZBTB48|ENSG00000204859|transcript|ENST00000488936|protein_coding||c.*850G>T|||||850|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|KLHL21|ENSG00000162413|transcript|ENST00000377663|protein_coding||c.*6410C>A|||||1769|,T|downstream_gene_variant|MODIFIER|KLHL21|ENSG00000162413|transcript|ENST00000467612|protein_coding||c.*4410C>A|||||4238|,T|downstream_gene_variant|MODIFIER|KLHL21|ENSG00000162413|transcript|ENST00000496707|protein_coding||c.*4426C>A|||||4426|WARNING_TRANSCRIPT_INCOMPLETE,T|non_coding_transcript_exon_variant|MODIFIER|ZBTB48|ENSG00000204859|transcript|ENST00000482360|retained_intron|7/7|n.2159G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|ZBTB48|ENSG00000204859|transcript|ENST00000498342|retained_intron|3/3|n.2136G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|ZBTB48|ENSG00000204859|transcript|ENST00000466941|retained_intron|2/2|n.198G>T|||||| GT:AD:AF:DP 0/1:66,3:0.057:69 0/0:57,0:0:57 | |
| chr1 7807910 . G A . t_lod_fstar ClippingRankSum=0;DP=176;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.74;ReadPosRankSum=0.55;TLOD=4.35;ANN=A|intron_variant|MODIFIER|CAMTA1|ENSG00000171735|transcript|ENST00000303635|protein_coding|19/22|c.4689+69G>A||||||,A|intron_variant|MODIFIER|CAMTA1|ENSG00000171735|transcript|ENST00000439411|protein_coding|19/21|c.4647+69G>A||||||,A|intron_variant|MODIFIER|CAMTA1|ENSG00000171735|transcript|ENST00000495233|protein_coding|7/10|c.1557+69G>A||||||,A|intron_variant|MODIFIER|CAMTA1|ENSG00000171735|transcript|ENST00000490905|protein_coding|3/5|c.384+69G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|CAMTA1|ENSG00000171735|transcript|ENST00000476864|protein_coding|3/5|c.381+69G>A|||||| GT:AD:AF:DP 0/1:124,4:0.031:128 0/0:45,0:0:45 | |
| chr1 8385485 . GA G . PASS ClippingRankSum=0;DP=88;ECNT=1;FS=1;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60.37;MQ0=0;MQRankSum=2.955;NLOD=2.74;ReadPosRankSum=-4.494;TLOD=9.46;ANN=G|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000252254|transcript|ENST00000516445|misc_RNA||n.-2641delA|||||2641|,G|upstream_gene_variant|MODIFIER|SLC45A1|ENSG00000162426|transcript|ENST00000497660|retained_intron||n.-4712delA|||||4712|,G|intron_variant|MODIFIER|SLC45A1|ENSG00000162426|transcript|ENST00000377479|protein_coding|3/8|c.592+45delA||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|SLC45A1|ENSG00000162426|transcript|ENST00000471889|protein_coding|3/8|c.490+45delA||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|SLC45A1|ENSG00000162426|transcript|ENST00000289877|protein_coding|2/7|c.490+45delA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:26,18:0.406:44 0/0:32,2:0.087:34 | |
| chr1 8716283 . TTC T . t_lod_fstar ClippingRankSum=0;DP=229;ECNT=1;FS=1.871;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=58.3;MQ0=0;MQRankSum=0.758;NLOD=10.67;ReadPosRankSum=-0.995;TLOD=5.52;ANN=T|frameshift_variant|HIGH|RERE|ENSG00000142599|transcript|ENST00000337907|protein_coding|3/24|c.72_73delGA|p.Asp27fs|708/8026|72/4701|24/1566||,T|frameshift_variant|HIGH|RERE|ENSG00000142599|transcript|ENST00000400907|protein_coding|1/15|c.72_73delGA|p.Asp27fs|147/2973|72/1755|24/584||,T|frameshift_variant|HIGH|RERE|ENSG00000142599|transcript|ENST00000400908|protein_coding|2/23|c.72_73delGA|p.Asp27fs|701/5790|72/4701|24/1566||,T|frameshift_variant|HIGH|RERE|ENSG00000142599|transcript|ENST00000468247|protein_coding|2/2|c.72_73delGA|p.Asp27fs|382/414|72/105|24/34||WARNING_TRANSCRIPT_NO_STOP_CODON,T|non_coding_transcript_exon_variant|MODIFIER|RERE|ENSG00000142599|transcript|ENST00000480342|retained_intron|2/11|n.624_625delGA||||||;LOF=(RERE|ENSG00000142599|18|0.06) GT:AD:AF:DP 0/1:119,3:0.033:122 0/0:67,2:0.033:69 | |
| chr1 12016940 . G T . t_lod_fstar ClippingRankSum=0;DP=46;ECNT=1;FS=2.407;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.31;ReadPosRankSum=0.041;TLOD=4.09;ANN=T|downstream_gene_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000449038|protein_coding||c.*4192G>T|||||4192|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000358133|processed_transcript||n.*2116G>T|||||2116|,T|intron_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000376369|protein_coding|7/19|c.785-34G>T||||||,T|intron_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000485046|processed_transcript|6/8|n.687-34G>T||||||,T|intron_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000429000|protein_coding|6/7|c.644-207G>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,T|intron_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000196061|protein_coding|6/18|c.644-34G>T||||||,T|intron_variant|MODIFIER|PLOD1|ENSG00000083444|transcript|ENST00000465920|retained_intron|1/3|n.594-34G>T|||||| GT:AD:AF:DP 0/1:28,4:0.095:32 0/0:14,0:0:14 | |
| chr1 12065800 . C T . t_lod_fstar ClippingRankSum=0;DP=116;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.72;ReadPosRankSum=1.276;TLOD=5.26;ANN=T|missense_variant|MODERATE|MFN2|ENSG00000116688|transcript|ENST00000235329|protein_coding|15/19|c.1528C>T|p.Arg510Trp|1850/4539|1528/2274|510/757||,T|missense_variant|MODERATE|MFN2|ENSG00000116688|transcript|ENST00000444836|protein_coding|14/18|c.1528C>T|p.Arg510Trp|1836/4531|1528/2274|510/757|| GT:AD:AF:DP 0/1:69,5:0.058:74 0/0:42,0:0:42 | |
| chr1 12516138 . G T . t_lod_fstar ClippingRankSum=0;DP=150;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.94;ReadPosRankSum=-1.096;TLOD=4.61;ANN=T|missense_variant|MODERATE|VPS13D|ENSG00000048707|transcript|ENST00000358136|protein_coding|66/70|c.12418G>T|p.Ala4140Ser|12548/16318|12418/13167|4140/4388||,T|missense_variant|MODERATE|VPS13D|ENSG00000048707|transcript|ENST00000356315|protein_coding|65/69|c.12343G>T|p.Ala4115Ser|12473/16243|12343/13092|4115/4363||,T|missense_variant|MODERATE|VPS13D|ENSG00000048707|transcript|ENST00000011700|protein_coding|48/52|c.8881G>T|p.Ala2961Ser|8883/10969|8881/9630|2961/3209||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|VPS13D|ENSG00000048707|transcript|ENST00000543766|protein_coding|4/8|c.412G>T|p.Ala138Ser|412/2498|412/1161|138/386||,T|intron_variant|MODIFIER|VPS13D|ENSG00000048707|transcript|ENST00000496628|processed_transcript|15/18|n.1991+11G>T|||||| GT:AD:AF:DP 0/1:88,3:0.044:91 0/0:58,0:0:58 | |
| chr1 12854139 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=526;ECNT=3;FS=3.105;HCNT=6;MAX_ED=231;MIN_ED=1;MQ=51.17;MQ0=34;MQRankSum=-1.38;NLOD=2.51;ReadPosRankSum=-5.926;TLOD=14.91;ANN=T|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|3/4|c.363C>T|p.Ala121Ala|466/2160|363/1425|121/474||,T|upstream_gene_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding||c.-849C>T|||||701| GT:AD:AF:DP:PGT:PID 0/1:288,10:0.026:298:0|1:12854139_C_T 0/0:146,12:0.056:158:0|1:12854139_C_T | |
| chr1 12854140 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=528;ECNT=3;FS=3.11;HCNT=6;MAX_ED=231;MIN_ED=1;MQ=51.1;MQ0=34;MQRankSum=-1.34;NLOD=2.51;ReadPosRankSum=-6.002;TLOD=14.91;ANN=G|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|3/4|c.364C>G|p.Leu122Val|467/2160|364/1425|122/474||,G|upstream_gene_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding||c.-848C>G|||||700| GT:AD:AF:DP:PGT:PID 0/1:291,10:0.026:301:0|1:12854139_C_T 0/0:146,12:0.056:158:0|1:12854139_C_T | |
| chr1 12854370 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=802;ECNT=3;FS=18.378;HCNT=6;MAX_ED=231;MIN_ED=1;MQ=51.89;MQ0=48;MQRankSum=-6.07;NLOD=25.36;ReadPosRankSum=-6.033;TLOD=32.93;ANN=G|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|3/4|c.594A>G|p.Ser198Ser|697/2160|594/1425|198/474||,G|upstream_gene_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding||c.-618A>G|||||470| GT:AD:AF:DP 0/1:407,25:0.075:432 0/0:265,16:0.067:281 | |
| chr1 12854401 . G T . PASS ClippingRankSum=0;DP=603;ECNT=1;FS=5.193;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=53.93;MQ0=28;MQRankSum=-4.4;NLOD=36.41;ReadPosRankSum=-2.186;TLOD=8.47;ANN=T|stop_gained|HIGH|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|3/4|c.625G>T|p.Glu209*|728/2160|625/1425|209/474||,T|upstream_gene_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding||c.-587G>T|||||439|;LOF=(PRAMEF1|ENSG00000116721|2|0.50);NMD=(PRAMEF1|ENSG00000116721|2|0.50) GT:AD:AF:DP 0/1:327,8:0.031:335 0/0:209,5:0.03:214 | |
| chr1 12854938 . C T . t_lod_fstar ClippingRankSum=0;DP=273;ECNT=1;FS=1.162;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=38.95;MQ0=91;MQRankSum=-0.076;NLOD=5.88;ReadPosRankSum=0.688;TLOD=4.97;ANN=T|5_prime_UTR_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|1/2|c.-50C>T|||||50|,T|intron_variant|MODIFIER|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|3/3|c.866+296C>T|||||| GT:AD:AF:DP 0/1:94,5:0.042:99 0/0:67,7:0.077:74 | |
| chr1 12855789 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=429;ECNT=2;FS=5.582;HCNT=5;MAX_ED=33;MIN_ED=33;MQ=52.45;MQ0=13;MQRankSum=-1.66;NLOD=2.21;ReadPosRankSum=-0.787;TLOD=9.75;ANN=A|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1069G>A|p.Glu357Lys|1172/2160|1069/1425|357/474||,A|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.334G>A|p.Glu112Lys|482/1327|334/690|112/229|| GT:AD:AF:DP 0/1:250,8:0.025:258 0/0:135,8:0.07:143 | |
| chr1 12855822 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=392;ECNT=2;FS=0;HCNT=4;MAX_ED=33;MIN_ED=33;MQ=49.14;MQ0=15;MQRankSum=-0.502;NLOD=5.45;ReadPosRankSum=1.671;TLOD=9.19;ANN=A|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1102G>A|p.Ala368Thr|1205/2160|1102/1425|368/474||,A|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.367G>A|p.Ala123Thr|515/1327|367/690|123/229|| GT:AD:AF:DP 0/1:232,5:0.023:237 0/0:118,5:0.051:123 | |
| chr1 12855876 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=377;ECNT=4;FS=0;HCNT=9;MAX_ED=120;MIN_ED=114;MQ=46.58;MQ0=25;MQRankSum=0.325;NLOD=12.70;ReadPosRankSum=0.436;TLOD=7.87;ANN=C|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1156A>C|p.Arg386Arg|1259/2160|1156/1425|386/474||,C|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.421A>C|p.Arg141Arg|569/1327|421/690|141/229|| GT:AD:AF:DP 0/1:207,4:0.024:211 0/0:116,5:0.047:121 | |
| chr1 12855990 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=891;ECNT=4;FS=1.852;HCNT=6;MAX_ED=120;MIN_ED=114;MQ=46.41;MQ0=39;MQRankSum=2.727;NLOD=12.81;ReadPosRankSum=-3.06;TLOD=16.67;ANN=G|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1270C>G|p.Arg424Gly|1373/2160|1270/1425|424/474||,G|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.535C>G|p.Arg179Gly|683/1327|535/690|179/229|| GT:AD:AF:DP:PGT:PID 0/1:481,7:0.02:488:0|1:12855990_C_G 0/0:288,16:0.057:304:0|1:12855990_C_G | |
| chr1 12855995 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=914;ECNT=4;FS=0;HCNT=6;MAX_ED=120;MIN_ED=114;MQ=46.66;MQ0=37;MQRankSum=2.828;NLOD=10.12;ReadPosRankSum=-2.292;TLOD=16.62;ANN=T|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1275C>T|p.Val425Val|1378/2160|1275/1425|425/474||,T|synonymous_variant|LOW|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.540C>T|p.Val180Val|688/1327|540/690|180/229|| GT:AD:AF:DP:PGT:PID 0/1:492,7:0.02:499:0|1:12855990_C_G 0/0:299,17:0.06:316:0|1:12855990_C_G | |
| chr1 12855996 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=913;ECNT=4;FS=0;HCNT=6;MAX_ED=120;MIN_ED=114;MQ=46.78;MQ0=35;MQRankSum=2.789;NLOD=9.82;ReadPosRankSum=-2.121;TLOD=16.59;ANN=G|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000332296|protein_coding|4/4|c.1276A>G|p.Asn426Asp|1379/2160|1276/1425|426/474||,G|missense_variant|MODERATE|PRAMEF1|ENSG00000116721|transcript|ENST00000400814|protein_coding|2/2|c.541A>G|p.Asn181Asp|689/1327|541/690|181/229|| GT:AD:AF:DP:PGT:PID 0/1:489,7:0.02:496:0|1:12855990_C_G 0/0:302,17:0.06:319:0|1:12855990_C_G | |
| chr1 12887088 . A C . t_lod_fstar ClippingRankSum=0;DP=419;ECNT=1;FS=10.599;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=38.75;MQ0=149;MQRankSum=2.581;NLOD=5.48;ReadPosRankSum=-0.458;TLOD=4.37;ANN=C|upstream_gene_variant|MODIFIER|RP5-845O24.8|ENSG00000228338|transcript|ENST00000438401|lincRNA||n.-4066T>G|||||4066|,C|intron_variant|MODIFIER|PRAMEF11|ENSG00000204513|transcript|ENST00000535591|protein_coding|3/3|c.749+20T>G||||||,C|intron_variant|MODIFIER|PRAMEF11|ENSG00000204513|transcript|ENST00000437584|protein_coding|3/3|c.749+20T>G||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:148,4:0.036:152 0/0:87,17:0.163:104 | |
| chr1 12887739 . C T . t_lod_fstar ClippingRankSum=0;DP=310;ECNT=1;FS=20.554;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=58.01;MQ0=8;MQRankSum=-6.97;NLOD=6.89;ReadPosRankSum=-1.946;TLOD=4.83;ANN=T|upstream_gene_variant|MODIFIER|RP5-845O24.8|ENSG00000228338|transcript|ENST00000438401|lincRNA||n.-4717G>A|||||4717|,T|intron_variant|MODIFIER|PRAMEF11|ENSG00000204513|transcript|ENST00000535591|protein_coding|2/3|c.168-50G>A||||||,T|intron_variant|MODIFIER|PRAMEF11|ENSG00000204513|transcript|ENST00000437584|protein_coding|2/3|c.168-50G>A||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:223,4:0.025:227 0/0:61,4:0.064:65 | |
| chr1 12898677 . G A . PASS ClippingRankSum=0;DP=488;ECNT=1;FS=18.538;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=50.09;MQ0=30;MQRankSum=-2.422;NLOD=4.89;ReadPosRankSum=0.426;TLOD=33.33;ANN=A|non_coding_transcript_exon_variant|MODIFIER|RP5-845O24.3|ENSG00000231103|transcript|ENST00000438176|unprocessed_pseudogene|3/4|n.996C>T|||||| GT:AD:AF:DP 0/1:320,12:0.05:332 0/0:117,5:0.062:122 | |
| chr1 12907742 . G A . t_lod_fstar ClippingRankSum=0;DP=242;ECNT=1;FS=23.646;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=57.78;MQ0=7;MQRankSum=-4.515;NLOD=4.04;ReadPosRankSum=-1.973;TLOD=6.00;ANN=A|missense_variant|MODERATE|HNRNPCL1|ENSG00000179172|transcript|ENST00000317869|protein_coding|2/2|c.401C>T|p.Pro134Leu|627/1108|401/882|134/293|| GT:AD:AF:DP 0/1:142,4:0.035:146 0/0:79,5:0.081:84 | |
| chr1 12918986 . G T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=138;ECNT=5;FS=6.031;HCNT=8;MAX_ED=82;MIN_ED=11;MQ=58.75;MQ0=2;MQRankSum=-5.33;NLOD=3.33;ReadPosRankSum=-1.613;TLOD=4.90;ANN=T|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/4|c.122G>T|p.Arg41Met|209/1642|122/1425|41/474|| GT:AD:AF:DP:PGT:PID 0/1:101,2:0.024:103:0|1:12918986_G_T 0/0:31,1:0.038:32:0|1:12918986_G_T | |
| chr1 12918997 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=146;ECNT=5;FS=4.345;HCNT=8;MAX_ED=82;MIN_ED=11;MQ=58.72;MQ0=2;MQRankSum=-7.936;NLOD=4.53;ReadPosRankSum=-1.682;TLOD=7.83;ANN=C|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/4|c.133A>C|p.Ser45Arg|220/1642|133/1425|45/474|| GT:AD:AF:DP:PGT:PID 0/1:104,4:0.034:108:0|1:12918986_G_T 0/0:34,1:0.033:35:0|1:12918986_G_T | |
| chr1 12919022 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=162;ECNT=5;FS=6.436;HCNT=8;MAX_ED=82;MIN_ED=11;MQ=58.93;MQ0=2;MQRankSum=-10.08;NLOD=6.64;ReadPosRankSum=-1.74;TLOD=26.49;ANN=T|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/4|c.158C>T|p.Thr53Met|245/1642|158/1425|53/474|| GT:AD:AF:DP:PGT:PID 0/1:105,11:0.096:116:0|1:12918986_G_T 0/0:42,1:0.027:43:0|1:12918986_G_T | |
| chr1 12919041 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=185;ECNT=5;FS=5.455;HCNT=8;MAX_ED=82;MIN_ED=11;MQ=58.7;MQ0=2;MQRankSum=-9.517;NLOD=2.86;ReadPosRankSum=0.896;TLOD=22.84;ANN=A|stop_gained|HIGH|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/4|c.177G>A|p.Trp59*|264/1642|177/1425|59/474||;LOF=(PRAMEF2|ENSG00000120952|1|1.00);NMD=(PRAMEF2|ENSG00000120952|1|1.00) GT:AD:AF:DP:PGT:PID 0/1:115,12:0.082:127:0|1:12918986_G_T 0/0:48,3:0.056:51:0|1:12918986_G_T | |
| chr1 12919068 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=199;ECNT=5;FS=4.09;HCNT=21;MAX_ED=82;MIN_ED=11;MQ=58.04;MQ0=4;MQRankSum=-11.031;NLOD=3.40;ReadPosRankSum=0.749;TLOD=27.81;ANN=A|synonymous_variant|LOW|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/4|c.204G>A|p.Ser68Ser|291/1642|204/1425|68/474|| GT:AD:AF:DP 0/1:109,20:0.149:129 0/0:58,5:0.067:63 | |
| chr1 12919536 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=320;ECNT=4;FS=40.984;HCNT=15;MAX_ED=53;MIN_ED=38;MQ=49.47;MQ0=17;MQRankSum=-0.958;NLOD=8.63;ReadPosRankSum=0.9;TLOD=13.94;ANN=T|intron_variant|MODIFIER|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|2/3|c.288-12C>T|||||| GT:AD:AF:DP 0/1:144,8:0.066:152 0/0:129,6:0.057:135 | |
| chr1 12919574 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=389;ECNT=4;FS=41.334;HCNT=12;MAX_ED=53;MIN_ED=38;MQ=52.04;MQ0=15;MQRankSum=-2.019;NLOD=18.42;ReadPosRankSum=-0.019;TLOD=14.46;ANN=A|stop_gained|HIGH|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|3/4|c.314T>A|p.Leu105*|401/1642|314/1425|105/474||;LOF=(PRAMEF2|ENSG00000120952|1|1.00);NMD=(PRAMEF2|ENSG00000120952|1|1.00) GT:AD:AF:DP:PGT:PID 0/1:200,6:0.033:206:0|1:12919574_T_A 0/0:148,4:0.032:152:0|1:12919574_T_A | |
| chr1 12919581 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=403;ECNT=4;FS=36.562;HCNT=12;MAX_ED=53;MIN_ED=38;MQ=53.1;MQ0=12;MQRankSum=-1.883;NLOD=19.33;ReadPosRankSum=-0.043;TLOD=12.56;ANN=C|synonymous_variant|LOW|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|3/4|c.321T>C|p.Asp107Asp|408/1642|321/1425|107/474|| GT:AD:AF:DP:PGT:PID 0/1:216,5:0.027:221:0|1:12919574_T_A 0/0:151,4:0.031:155:0|1:12919574_T_A | |
| chr1 12919589 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=406;ECNT=4;FS=33.312;HCNT=12;MAX_ED=53;MIN_ED=38;MQ=53.92;MQ0=10;MQRankSum=-2.443;NLOD=23.72;ReadPosRankSum=-0.588;TLOD=12.54;ANN=G|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|3/4|c.329A>G|p.Glu110Gly|416/1642|329/1425|110/474|| GT:AD:AF:DP:PGT:PID 0/1:224,5:0.027:229:0|1:12919574_T_A 0/0:151,3:0.023:154:0|1:12919574_T_A | |
| chr1 12921133 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=378;ECNT=3;FS=22.335;HCNT=3;MAX_ED=62;MIN_ED=4;MQ=58.6;MQ0=2;MQRankSum=-2.322;NLOD=11.48;ReadPosRankSum=-3.138;TLOD=9.71;ANN=A|synonymous_variant|LOW|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.924G>A|p.Glu308Glu|1011/1642|924/1425|308/474|| GT:AD:AF:DP:PGT:PID 0/1:247,4:0.023:251:0|1:12921133_G_A 0/0:118,3:0.035:121:0|1:12921133_G_A | |
| chr1 12921137 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=358;ECNT=3;FS=16.13;HCNT=3;MAX_ED=62;MIN_ED=4;MQ=58.68;MQ0=2;MQRankSum=-1.437;NLOD=9.68;ReadPosRankSum=-2.951;TLOD=9.72;ANN=A|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.928T>A|p.Leu310Met|1015/1642|928/1425|310/474|| GT:AD:AF:DP:PGT:PID 0/1:239,2:0.023:241:0|1:12921133_G_A 0/0:109,3:0.038:112:0|1:12921133_G_A | |
| chr1 12921195 . A T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=284;ECNT=3;FS=18.947;HCNT=6;MAX_ED=62;MIN_ED=4;MQ=59.24;MQ0=1;MQRankSum=-6.033;NLOD=4.40;ReadPosRankSum=-2.833;TLOD=6.10;ANN=T|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.986A>T|p.Tyr329Phe|1073/1642|986/1425|329/474|| GT:AD:AF:DP 0/1:195,4:0.028:199 0/0:76,7:0.095:83 | |
| chr1 12921479 . C G . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=208;ECNT=3;FS=2.59;HCNT=9;MAX_ED=6;MIN_ED=5;MQ=40.12;MQ0=60;MQRankSum=-2.24;NLOD=7.52;ReadPosRankSum=1.139;TLOD=8.28;ANN=G|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.1270C>G|p.Arg424Gly|1357/1642|1270/1425|424/474|| GT:AD:AF:DP:PGT:PID 0/1:66,3:0.048:69:0|1:12921479_C_G 0/0:62,0:0:62:0|1:12921479_C_G | |
| chr1 12921484 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=202;ECNT=3;FS=0;HCNT=9;MAX_ED=6;MIN_ED=5;MQ=40;MQ0=62;MQRankSum=-1.512;NLOD=7.22;ReadPosRankSum=0.583;TLOD=8.33;ANN=T|synonymous_variant|LOW|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.1275C>T|p.Val425Val|1362/1642|1275/1425|425/474|| GT:AD:AF:DP:PGT:PID 0/1:60,3:0.05:63:0|1:12921479_C_G 0/0:61,1:0.021:62:0|1:12921479_C_G | |
| chr1 12921485 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=202;ECNT=3;FS=0;HCNT=9;MAX_ED=6;MIN_ED=5;MQ=39.86;MQ0=63;MQRankSum=-1.511;NLOD=7.22;ReadPosRankSum=0.651;TLOD=8.37;ANN=G|missense_variant|MODERATE|PRAMEF2|ENSG00000120952|transcript|ENST00000240189|protein_coding|4/4|c.1276A>G|p.Asn426Asp|1363/1642|1276/1425|426/474|| GT:AD:AF:DP:PGT:PID 0/1:59,3:0.052:62:0|1:12921479_C_G 0/0:61,1:0.021:62:0|1:12921479_C_G | |
| chr1 12939548 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=703;ECNT=2;FS=10.353;HCNT=7;MAX_ED=14;MIN_ED=14;MQ=53.69;MQ0=28;MQRankSum=-1.553;NLOD=33.86;ReadPosRankSum=2.4;TLOD=7.91;ANN=C|synonymous_variant|LOW|PRAMEF4|ENSG00000243073|transcript|ENST00000235349|protein_coding|4/4|c.1254C>G|p.Pro418Pro|1325/1828|1254/1437|418/478|| GT:AD:AF:DP 0/1:370,6:0.022:376 0/0:244,7:0.036:251 | |
| chr1 12939562 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=633;ECNT=2;FS=13.367;HCNT=7;MAX_ED=14;MIN_ED=14;MQ=54.44;MQ0=29;MQRankSum=-1.833;NLOD=27.64;ReadPosRankSum=1.462;TLOD=8.16;ANN=C|missense_variant|MODERATE|PRAMEF4|ENSG00000243073|transcript|ENST00000235349|protein_coding|4/4|c.1240C>G|p.Leu414Val|1311/1828|1240/1437|414/478|| GT:AD:AF:DP 0/1:365,6:0.021:371 0/0:213,7:0.04:220 | |
| chr1 12952767 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=297;ECNT=4;FS=2.401;HCNT=10;MAX_ED=8;MIN_ED=3;MQ=52.79;MQ0=2;MQRankSum=-3.948;NLOD=3.34;ReadPosRankSum=-4.243;TLOD=16.10;ANN=G|missense_variant|MODERATE|PRAMEF10|ENSG00000187545|transcript|ENST00000235347|protein_coding|4/4|c.1405G>C|p.Asp469His|1485/1525|1405/1425|469/474|| GT:AD:AF:DP:PGT:PID 0/1:214,10:0.041:224:0|1:12952767_C_G 0/0:65,3:0.067:68:0|1:12952767_C_G | |
| chr1 12952770 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=299;ECNT=4;FS=1.137;HCNT=10;MAX_ED=8;MIN_ED=3;MQ=52.75;MQ0=2;MQRankSum=-4.391;NLOD=3.34;ReadPosRankSum=-4.157;TLOD=16.13;ANN=T|missense_variant|MODERATE|PRAMEF10|ENSG00000187545|transcript|ENST00000235347|protein_coding|4/4|c.1402G>A|p.Val468Met|1482/1525|1402/1425|468/474|| GT:AD:AF:DP:PGT:PID 0/1:216,10:0.042:226:0|1:12952767_C_G 0/0:66,2:0.068:68:0|1:12952767_C_G | |
| chr1 12952771 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=297;ECNT=4;FS=1.137;HCNT=10;MAX_ED=8;MIN_ED=3;MQ=52.74;MQ0=2;MQRankSum=-4.357;NLOD=3.64;ReadPosRankSum=-4.332;TLOD=16.10;ANN=G|missense_variant|MODERATE|PRAMEF10|ENSG00000187545|transcript|ENST00000235347|protein_coding|4/4|c.1401A>C|p.Lys467Asn|1481/1525|1401/1425|467/474|| GT:AD:AF:DP:PGT:PID 0/1:215,10:0.041:225:0|1:12952767_C_G 0/0:65,2:0.044:67:0|1:12952767_C_G | |
| chr1 12952775 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=291;ECNT=4;FS=1.267;HCNT=10;MAX_ED=8;MIN_ED=3;MQ=52.88;MQ0=2;MQRankSum=-3.448;NLOD=4.20;ReadPosRankSum=-3.824;TLOD=22.39;ANN=C|missense_variant|MODERATE|PRAMEF10|ENSG00000187545|transcript|ENST00000235347|protein_coding|4/4|c.1397A>G|p.Glu466Gly|1477/1525|1397/1425|466/474|| GT:AD:AF:DP:PGT:PID 0/1:212,7:0.053:219:0|1:12952767_C_G 0/0:65,2:0.043:67:0|1:12952767_C_G | |
| chr1 12979665 . C T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=311;ECNT=5;FS=1.956;HCNT=20;MAX_ED=37;MIN_ED=6;MQ=48.66;MQ0=2;MQRankSum=-3.497;NLOD=16.56;ReadPosRankSum=1.869;TLOD=4.34;ANN=T|splice_region_variant&intron_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000330881|protein_coding|2/2|c.864-7C>T||||||,T|splice_region_variant&intron_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000361079|protein_coding|3/3|c.864-7C>T||||||,T|upstream_gene_variant|MODIFIER|RNU6-1072P|ENSG00000207434|transcript|ENST00000384703|snRNA||n.-2709C>T|||||2709| GT:AD:AF:DP:PGT:PID 0/1:212,4:0.013:216:0|1:12979665_C_T 0/0:83,0:0:83:0|1:12979665_C_T | |
| chr1 12979671 . G A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=322;ECNT=5;FS=1.894;HCNT=20;MAX_ED=37;MIN_ED=6;MQ=48.61;MQ0=2;MQRankSum=-3.503;NLOD=17.46;ReadPosRankSum=1.741;TLOD=4.32;ANN=A|splice_acceptor_variant&intron_variant|HIGH|PRAMEF7|ENSG00000204510|transcript|ENST00000330881|protein_coding|2/2|c.864-1G>A||||||,A|splice_acceptor_variant&intron_variant|HIGH|PRAMEF7|ENSG00000204510|transcript|ENST00000361079|protein_coding|3/3|c.864-1G>A||||||,A|upstream_gene_variant|MODIFIER|RNU6-1072P|ENSG00000207434|transcript|ENST00000384703|snRNA||n.-2703G>A|||||2703|;LOF=(PRAMEF7|ENSG00000204510|2|1.00) GT:AD:AF:DP:PGT:PID 0/1:224,4:0.012:228:0|1:12979665_C_T 0/0:83,0:0:83:0|1:12979665_C_T | |
| chr1 12979685 . T C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=349;ECNT=5;FS=0;HCNT=20;MAX_ED=37;MIN_ED=6;MQ=48.48;MQ0=3;MQRankSum=-3.441;NLOD=17.76;ReadPosRankSum=1.742;TLOD=4.22;ANN=C|missense_variant|MODERATE|PRAMEF7|ENSG00000204510|transcript|ENST00000330881|protein_coding|3/3|c.877T>C|p.Ser293Pro|877/1425|877/1425|293/474||,C|missense_variant|MODERATE|PRAMEF7|ENSG00000204510|transcript|ENST00000361079|protein_coding|4/4|c.877T>C|p.Ser293Pro|960/1844|877/1425|293/474||,C|upstream_gene_variant|MODIFIER|RNU6-1072P|ENSG00000207434|transcript|ENST00000384703|snRNA||n.-2689T>C|||||2689| GT:AD:AF:DP:PGT:PID 0/1:243,4:0.011:247:0|1:12979665_C_T 0/0:90,0:0:90:0|1:12979665_C_T | |
| chr1 12979699 . C T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=387;ECNT=5;FS=0;HCNT=20;MAX_ED=37;MIN_ED=6;MQ=48.55;MQ0=4;MQRankSum=-3.38;NLOD=21.37;ReadPosRankSum=-0.155;TLOD=4.16;ANN=T|synonymous_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000330881|protein_coding|3/3|c.891C>T|p.Val297Val|891/1425|891/1425|297/474||,T|synonymous_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000361079|protein_coding|4/4|c.891C>T|p.Val297Val|974/1844|891/1425|297/474||,T|upstream_gene_variant|MODIFIER|RNU6-1072P|ENSG00000207434|transcript|ENST00000384703|snRNA||n.-2675C>T|||||2675| GT:AD:AF:DP:PGT:PID 0/1:269,4:0.01:273:0|1:12979665_C_T 0/0:102,0:0:102:0|1:12979665_C_T | |
| chr1 12979702 . T C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=396;ECNT=5;FS=0;HCNT=20;MAX_ED=37;MIN_ED=6;MQ=48.56;MQ0=4;MQRankSum=-3.367;NLOD=21.67;ReadPosRankSum=-0.301;TLOD=4.16;ANN=C|synonymous_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000330881|protein_coding|3/3|c.894T>C|p.Val298Val|894/1425|894/1425|298/474||,C|synonymous_variant|LOW|PRAMEF7|ENSG00000204510|transcript|ENST00000361079|protein_coding|4/4|c.894T>C|p.Val298Val|977/1844|894/1425|298/474||,C|upstream_gene_variant|MODIFIER|RNU6-1072P|ENSG00000207434|transcript|ENST00000384703|snRNA||n.-2672T>C|||||2672| GT:AD:AF:DP:PGT:PID 0/1:275,4:0.01:279:0|1:12979665_C_T 0/0:105,0:0:105:0|1:12979665_C_T | |
| chr1 13172256 . C G . PASS ClippingRankSum=0;DP=1282;ECNT=1;FS=18.296;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=53.94;MQ0=55;MQRankSum=-8.362;NLOD=57.41;ReadPosRankSum=0.84;TLOD=51.68;ANN=G|non_coding_transcript_exon_variant|MODIFIER|RP13-221M14.4|ENSG00000236179|transcript|ENST00000458709|unprocessed_pseudogene|2/2|n.506G>C|||||| GT:AD:AF:DP 0/1:741,34:0.063:775 0/0:420,12:0.039:432 | |
| chr1 13183012 . G C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=178;ECNT=3;FS=10.914;HCNT=2;MAX_ED=3;MIN_ED=2;MQ=56.87;MQ0=5;MQRankSum=-4.514;NLOD=11.73;ReadPosRankSum=-2.092;TLOD=7.90;ANN=C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000449855|processed_pseudogene|2/2|n.1104C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000323770|processed_pseudogene|1/1|n.861C>G|||||| GT:AD:AF:DP:PGT:PID 0/1:112,3:0.036:115:0|1:13183012_G_C 0/0:57,0:0:57:0|1:13183012_G_C | |
| chr1 13183014 . T C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=178;ECNT=3;FS=10.739;HCNT=2;MAX_ED=3;MIN_ED=2;MQ=57.1;MQ0=5;MQRankSum=-4.756;NLOD=11.99;ReadPosRankSum=-2.231;TLOD=7.84;ANN=C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000449855|processed_pseudogene|2/2|n.1102A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000323770|processed_pseudogene|1/1|n.859A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:112,3:0.034:115:0|1:13183012_G_C 0/0:57,0:0:57:0|1:13183012_G_C | |
| chr1 13183015 . G C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=178;ECNT=3;FS=10.508;HCNT=2;MAX_ED=3;MIN_ED=2;MQ=57.45;MQ0=3;MQRankSum=-4.925;NLOD=11.64;ReadPosRankSum=-2.235;TLOD=7.88;ANN=C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000449855|processed_pseudogene|2/2|n.1101C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP5|ENSG00000179412|transcript|ENST00000323770|processed_pseudogene|1/1|n.858C>G|||||| GT:AD:AF:DP:PGT:PID 0/1:113,3:0.037:116:0|1:13183012_G_C 0/0:58,0:0:58:0|1:13183012_G_C | |
| chr1 13219066 . T C . PASS ClippingRankSum=0;DP=1309;ECNT=1;FS=9.501;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=44.27;MQ0=169;MQRankSum=-2.605;NLOD=36.57;ReadPosRankSum=-1.229;TLOD=55.11;ANN=C|missense_variant|MODERATE|PRAMEF26|ENSG00000229571|transcript|ENST00000423177|protein_coding|1/2|c.515A>G|p.His172Arg|516/1476|515/1143|172/380||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:540,57:0.098:597 0/0:445,38:0.083:483 | |
| chr1 13219498 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=994;ECNT=3;FS=9.4;HCNT=9;MAX_ED=133;MIN_ED=116;MQ=52.06;MQ0=38;MQRankSum=-0.335;NLOD=61.34;ReadPosRankSum=-0.763;TLOD=9.00;ANN=G|missense_variant|MODERATE|PRAMEF26|ENSG00000229571|transcript|ENST00000423177|protein_coding|1/2|c.83G>C|p.Cys28Ser|84/1476|83/1143|28/380||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:547,11:0.028:558 0/0:364,21:0.055:385 | |
| chr1 13219614 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=775;ECNT=3;FS=1.205;HCNT=14;MAX_ED=133;MIN_ED=116;MQ=51.75;MQ0=44;MQRankSum=-3.531;NLOD=14.28;ReadPosRankSum=1.195;TLOD=20.91;ANN=A|upstream_gene_variant|MODIFIER|PRAMEF26|ENSG00000229571|transcript|ENST00000423177|protein_coding||c.-34G>T|||||33|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|PRAMEF26-PRAMEF3|ENSG00000229571-ENSG00000204503|intergenic_region|ENSG00000229571-ENSG00000204503|||n.13219614C>A|||||| GT:AD:AF:DP:PGT:PID 0/1:407,19:0.032:426:0|1:13219614_C_A 0/0:256,23:0.077:279:0|1:13219614_C_A | |
| chr1 13219631 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=671;ECNT=3;FS=7.341;HCNT=14;MAX_ED=133;MIN_ED=116;MQ=52.73;MQ0=37;MQRankSum=-3.136;NLOD=9.46;ReadPosRankSum=-1.975;TLOD=30.45;ANN=T|upstream_gene_variant|MODIFIER|PRAMEF26|ENSG00000229571|transcript|ENST00000423177|protein_coding||c.-51G>A|||||50|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|PRAMEF26-PRAMEF3|ENSG00000229571-ENSG00000204503|intergenic_region|ENSG00000229571-ENSG00000204503|||n.13219631C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:365,14:0.043:379:0|1:13219614_C_A 0/0:215,19:0.076:234:0|1:13219614_C_A | |
| chr1 16354394 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=402;ECNT=4;FS=10.105;HCNT=22;MAX_ED=47;MIN_ED=39;MQ=46.93;MQ0=96;MQRankSum=-1.584;NLOD=10.11;ReadPosRankSum=3.366;TLOD=6.57;ANN=T|missense_variant|MODERATE|CLCNKA|ENSG00000186510|transcript|ENST00000331433|protein_coding|9/20|c.860C>T|p.Ala287Val|879/2475|860/2064|287/687||,T|missense_variant|MODERATE|CLCNKA|ENSG00000186510|transcript|ENST00000375692|protein_coding|10/21|c.860C>T|p.Ala287Val|988/2581|860/2061|287/686||,T|missense_variant|MODERATE|CLCNKA|ENSG00000186510|transcript|ENST00000420078|protein_coding|9/20|c.860C>T|p.Ala287Val|940/2530|860/2061|287/686||,T|missense_variant|MODERATE|CLCNKA|ENSG00000186510|transcript|ENST00000439316|protein_coding|8/19|c.731C>T|p.Ala244Val|788/1997|731/1935|244/644||,T|downstream_gene_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000495784|processed_transcript||n.*1303C>T|||||1303|,T|non_coding_transcript_exon_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000464764|processed_transcript|13/24|n.1423C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000491433|processed_transcript|3/8|n.276C>T|||||| GT:AD:AF:DP 0/1:164,9:0.042:173 0/0:102,17:0.126:119 | |
| chr1 16354433 . A AT . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=371;ECNT=4;FS=11.937;HCNT=20;MAX_ED=47;MIN_ED=39;MQ=51.76;MQ0=49;MQRankSum=-2.895;NLOD=3.96;ReadPosRankSum=-1.403;TLOD=10.33;ANN=AT|downstream_gene_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000495784|processed_transcript||n.*1342_*1343insT|||||1343|,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000331433|protein_coding|9/19|c.866+33_866+34insT||||||,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000464764|processed_transcript|13/23|n.1429+33_1429+34insT||||||,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000375692|protein_coding|10/20|c.866+33_866+34insT||||||,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000420078|protein_coding|9/19|c.866+33_866+34insT||||||,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000439316|protein_coding|8/18|c.737+33_737+34insT||||||,AT|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000491433|processed_transcript|3/7|n.282+33_282+34insT|||||| GT:AD:AF:DP:PGT:PID 0/1:196,8:0.032:204:0|1:16354433_A_AT 0/0:91,12:0.12:103:0|1:16354433_A_AT | |
| chr1 16354435 . A T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=364;ECNT=4;FS=11.857;HCNT=20;MAX_ED=47;MIN_ED=39;MQ=52.1;MQ0=45;MQRankSum=-2.944;NLOD=3.66;ReadPosRankSum=-1.769;TLOD=10.29;ANN=T|downstream_gene_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000495784|processed_transcript||n.*1344A>T|||||1344|,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000331433|protein_coding|9/19|c.866+35A>T||||||,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000464764|processed_transcript|13/23|n.1429+35A>T||||||,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000375692|protein_coding|10/20|c.866+35A>T||||||,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000420078|protein_coding|9/19|c.866+35A>T||||||,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000439316|protein_coding|8/18|c.737+35A>T||||||,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000491433|processed_transcript|3/7|n.282+35A>T|||||| GT:AD:AF:DP:PGT:PID 0/1:195,8:0.031:203:0|1:16354433_A_AT 0/0:92,12:0.122:104:0|1:16354433_A_AT | |
| chr1 16354441 . TC T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=367;ECNT=4;FS=9.922;HCNT=20;MAX_ED=47;MIN_ED=39;MQ=52.8;MQ0=39;MQRankSum=-3.219;NLOD=4.86;ReadPosRankSum=-2.355;TLOD=13.33;ANN=T|downstream_gene_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000495784|processed_transcript||n.*1351delC|||||1351|,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000331433|protein_coding|9/19|c.866+47delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000464764|processed_transcript|13/23|n.1429+47delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000375692|protein_coding|10/20|c.866+47delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000420078|protein_coding|9/19|c.866+47delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000439316|protein_coding|8/18|c.737+47delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|CLCNKA|ENSG00000186510|transcript|ENST00000491433|processed_transcript|3/7|n.282+47delC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:201,8:0.039:209:0|1:16354433_A_AT 0/0:97,11:0.104:108:0|1:16354433_A_AT | |
| chr1 16812113 . G A . t_lod_fstar ClippingRankSum=0;DP=164;ECNT=1;FS=11.276;HCNT=38;MAX_ED=.;MIN_ED=.;MQ=58.41;MQ0=2;MQRankSum=-8.729;NLOD=4.63;ReadPosRankSum=-3.539;TLOD=6.10;ANN=A|upstream_gene_variant|MODIFIER|CROCCP3|ENSG00000080947|transcript|ENST00000591316|retained_intron||n.-2277C>T|||||2277|,A|non_coding_transcript_exon_variant|MODIFIER|CROCCP3|ENSG00000080947|transcript|ENST00000263511|processed_transcript|7/15|n.1439C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|CROCCP3|ENSG00000080947|transcript|ENST00000591348|processed_transcript|5/12|n.456C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|CROCCP3|ENSG00000080947|transcript|ENST00000420820|transcribed_unprocessed_pseudogene|7/14|n.808C>T|||||| GT:AD:AF:DP 0/1:101,4:0.058:105 0/0:49,4:0.077:53 | |
| chr1 16863382 . A T . t_lod_fstar ClippingRankSum=0;DP=175;ECNT=1;FS=8.43;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=58.58;MQ0=1;MQRankSum=-5.174;NLOD=13.50;ReadPosRankSum=-1.07;TLOD=4.10;ANN=T|upstream_gene_variant|MODIFIER|U1|ENSG00000233421|transcript|ENST00000415386|lincRNA||n.-1238T>A|||||1238|,T|upstream_gene_variant|MODIFIER|FAM231B|ENSG00000268674|transcript|ENST00000601199|protein_coding||c.-2179A>T|||||2179|,T|upstream_gene_variant|MODIFIER|U1|ENSG00000233421|transcript|ENST00000516290|snRNA||n.-2663T>A|||||2663|,T|intergenic_region|MODIFIER|U1-FAM231B|ENSG00000233421-ENSG00000268674|intergenic_region|ENSG00000233421-ENSG00000268674|||n.16863382A>T|||||| GT:AD:AF:DP 0/1:102,3:0.041:105 0/0:66,1:0.022:67 | |
| chr1 16890441 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1117;ECNT=3;FS=1.87;HCNT=20;MAX_ED=198;MIN_ED=43;MQ=59.64;MQ0=0;MQRankSum=-22.392;NLOD=50.91;ReadPosRankSum=-4.279;TLOD=21.33;ANN=T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|29/29|c.3417G>A|p.Gln1139Gln|4305/5932|3417/3420|1139/1139||,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay||c.*18772G>A|||||907|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.*9198G>A|||||2494|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.*3382G>A|||||2494| GT:AD:AF:DP 0/1:708,22:0.033:730 0/0:336,9:0.03:345 | |
| chr1 16890484 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1312;ECNT=3;FS=2.986;HCNT=27;MAX_ED=198;MIN_ED=43;MQ=59.94;MQ0=0;MQRankSum=-5.182;NLOD=24.97;ReadPosRankSum=-1.986;TLOD=22.96;ANN=C|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|29/29|c.3374C>G|p.Thr1125Arg|4262/5932|3374/3420|1125/1139||,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay||c.*18729C>G|||||864|,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.*9155C>G|||||2451|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.*3339C>G|||||2451| GT:AD:AF:DP 0/1:852,33:0.03:885 0/0:358,28:0.088:386 | |
| chr1 16890639 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=973;ECNT=3;FS=0;HCNT=15;MAX_ED=198;MIN_ED=43;MQ=57.08;MQ0=4;MQRankSum=-8.743;NLOD=5.15;ReadPosRankSum=0.384;TLOD=47.49;ANN=T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|29/29|c.3219G>A|p.Leu1073Leu|4107/5932|3219/3420|1073/1139||,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay||c.*18574G>A|||||709|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.*9000G>A|||||2296|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.*3184G>A|||||2296|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*10344G>A|||||4944|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:631,40:0.063:671 0/0:263,22:0.087:285 | |
| chr1 16890712 . C T . t_lod_fstar ClippingRankSum=0;DP=704;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=56.99;MQ0=3;MQRankSum=0.072;NLOD=22.92;ReadPosRankSum=-3.363;TLOD=5.09;ANN=T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay||c.*18501G>A|||||636|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.*8927G>A|||||2223|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.*3111G>A|||||2223|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*10271G>A|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|28/28|c.3177-31G>A|||||| GT:AD:AF:DP 0/1:433,9:0.015:442 0/0:204,8:0.044:212 | |
| chr1 16893736 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1329;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.48;MQ0=0;MQRankSum=-3.973;NLOD=56.76;ReadPosRankSum=0.584;TLOD=25.64;ANN=T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2777C>A|p.Pro926His|3665/5932|2777/3420|926/1139||,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1645C>A|||||15477|,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*329C>A|||||5903|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*87C>A|||||87|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7247C>A|||||1847|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:888,13:0.018:901:0|1:16893736_G_T 0/0:414,10:0.027:424:0|1:16893736_G_T | |
| chr1 16893742 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1322;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.48;MQ0=0;MQRankSum=-4.566;NLOD=55.53;ReadPosRankSum=0.554;TLOD=25.57;ANN=A|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2771G>T|p.Cys924Phe|3659/5932|2771/3420|924/1139||,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1639G>T|||||15471|,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*323G>T|||||5897|WARNING_TRANSCRIPT_NO_START_CODON,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*81G>T|||||81|,A|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7241G>T|||||1841|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:876,13:0.018:889:0|1:16893736_G_T 0/0:422,7:0.027:429:0|1:16893736_G_T | |
| chr1 16893752 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1309;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.47;MQ0=0;MQRankSum=-4.952;NLOD=57.00;ReadPosRankSum=-0.75;TLOD=28.39;ANN=G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2761A>C|p.Thr921Pro|3649/5932|2761/3420|921/1139||,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1629A>C|||||15461|,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*313A>C|||||5887|WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*71A>C|||||71|,G|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7231A>C|||||1831|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:872,11:0.02:883:0|1:16893736_G_T 0/0:415,7:0.024:422:0|1:16893736_G_T | |
| chr1 16893753 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1308;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.46;MQ0=0;MQRankSum=-4.949;NLOD=57.30;ReadPosRankSum=-0.961;TLOD=22.89;ANN=T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2760G>A|p.Leu920Leu|3648/5932|2760/3420|920/1139||,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1628G>A|||||15460|,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*312G>A|||||5886|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*70G>A|||||70|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7230G>A|||||1830|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:873,11:0.017:884:0|1:16893736_G_T 0/0:413,7:0.024:420:0|1:16893736_G_T | |
| chr1 16893760 . AG A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1270;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.43;MQ0=0;MQRankSum=-3.927;NLOD=57.60;ReadPosRankSum=-1.39;TLOD=14.90;ANN=A|frameshift_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2752delC|p.Glu919fs|3640/5932|2752/3420|918/1139||,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1620delC|||||15452|,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*304delC|||||5878|WARNING_TRANSCRIPT_NO_START_CODON,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*62delC|||||62|,A|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7222delC|||||1822|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(NBPF1|ENSG00000219481|9|0.11) GT:AD:AF:DP:PGT:PID 0/1:855,8:0.011:863:0|1:16893736_G_T 0/0:396,7:0.024:403:0|1:16893736_G_T | |
| chr1 16893763 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1261;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.32;MQ0=0;MQRankSum=-3.772;NLOD=55.19;TLOD=15.00;ANN=G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2750A>C|p.Tyr917Ser|3638/5932|2750/3420|917/1139||,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1618A>C|||||15450|,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*302A>C|||||5876|WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*60A>C|||||60|,G|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7220A>C|||||1820|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:850,8:0.012:858:0|1:16893736_G_T 0/0:392,7:0.024:399:0|1:16893736_G_T | |
| chr1 16893766 . C CA . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1253;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.2;MQ0=0;MQRankSum=-3.854;NLOD=53.69;ReadPosRankSum=-2.002;TLOD=15.03;ANN=CA|frameshift_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2746_2747insT|p.Gly916fs|3634/5932|2746/3420|916/1139||,CA|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1614_*1615insT|||||15446|,CA|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*298_*299insT|||||5872|WARNING_TRANSCRIPT_NO_START_CODON,CA|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*56_*57insT|||||56|,CA|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7216_*7217insT|||||1816|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(NBPF1|ENSG00000219481|9|0.11) GT:AD:AF:DP:PGT:PID 0/1:848,8:0.012:856:0|1:16893736_G_T 0/0:387,6:0.025:393:0|1:16893736_G_T | |
| chr1 16893767 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1243;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=58.19;MQ0=0;MQRankSum=-3.827;NLOD=59.09;ReadPosRankSum=-2.172;TLOD=15.03;ANN=T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2746G>A|p.Gly916Ser|3634/5932|2746/3420|916/1139||,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1614G>A|||||15446|,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*298G>A|||||5872|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*56G>A|||||56|,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7216G>A|||||1816|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:845,8:0.012:853:0|1:16893736_G_T 0/0:380,6:0.021:386:0|1:16893736_G_T | |
| chr1 16893771 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1203;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=57.94;MQ0=0;MQRankSum=-3.494;NLOD=55.48;ReadPosRankSum=-2.902;TLOD=15.00;ANN=C|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2742T>G|p.Pro914Pro|3630/5932|2742/3420|914/1139||,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1610T>G|||||15442|,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*294T>G|||||5868|WARNING_TRANSCRIPT_NO_START_CODON,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*52T>G|||||52|,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7212T>G|||||1812|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:825,8:0.012:833:0|1:16893736_G_T 0/0:360,6:0.022:366:0|1:16893736_G_T | |
| chr1 16893777 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1182;ECNT=11;FS=0;HCNT=6;MAX_ED=118;MIN_ED=6;MQ=57.74;MQ0=0;MQRankSum=-3.519;NLOD=53.66;ReadPosRankSum=-3.191;TLOD=15.11;ANN=C|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|25/29|c.2736A>G|p.Ser912Ser|3624/5932|2736/3420|912/1139||,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|16/19|c.*1604A>G|||||15436|,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|5/6|c.*288A>G|||||5862|WARNING_TRANSCRIPT_NO_START_CODON,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|8/9|c.*46A>G|||||46|,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7206A>G|||||1806|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:812,8:0.012:820:0|1:16893736_G_T 0/0:353,5:0.02:358:0|1:16893736_G_T | |
| chr1 16893854 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=641;ECNT=11;FS=0;HCNT=26;MAX_ED=118;MIN_ED=6;MQ=56.3;MQ0=1;MQRankSum=-2.149;NLOD=9.12;ReadPosRankSum=-0.198;TLOD=54.24;ANN=C|splice_region_variant&intron_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|24/28|c.2667-8T>G||||||,C|splice_region_variant&intron_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/18|c.*1535-8T>G||||||,C|splice_region_variant&intron_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/5|c.*219-8T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|splice_region_variant&intron_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|7/8|c.877-8T>G||||||,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*7129T>G|||||1729|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:372,50:0.117:422 0/0:194,20:0.086:214 | |
| chr1 16894472 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=5472;ECNT=3;FS=0;HCNT=7;MAX_ED=51;MIN_ED=4;MQ=40.48;MQ0=802;MQRankSum=-0.729;NLOD=92.59;ReadPosRankSum=6.251;TLOD=111.30;ANN=G|splice_donor_variant&intron_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|24/28|c.2666+2T>C||||||,G|splice_donor_variant&intron_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/18|c.*1534+2T>C||||||,G|splice_donor_variant&intron_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/5|c.*218+2T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|splice_donor_variant&intron_variant|HIGH|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|7/8|c.876+2T>C||||||,G|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*6511T>C|||||1111|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(NBPF1|ENSG00000219481|9|0.44) GT:AD:AF:DP:PGT:PID 0/1:2781,84:0.023:2865:0|1:16894472_A_G 0/0:1451,98:0.058:1549:0|1:16894472_A_G | |
| chr1 16894476 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=5498;ECNT=3;FS=0;HCNT=7;MAX_ED=51;MIN_ED=4;MQ=40.54;MQ0=809;MQRankSum=-0.722;NLOD=98.99;ReadPosRankSum=7.256;TLOD=111.24;ANN=C|missense_variant&splice_region_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|7/9|c.874C>G|p.Gln292Glu|874/1069|874/900|292/299||,C|splice_region_variant&synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|24/29|c.2664C>G|p.Pro888Pro|3552/5932|2664/3420|888/1139||,C|splice_region_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/19|c.*1532C>G||||||,C|splice_region_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/6|c.*216C>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/19|c.*1532C>G|||||14737|,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/6|c.*216C>G|||||5163|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*6507C>G|||||1107|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:2788,83:0.023:2871:0|1:16894472_A_G 0/0:1464,97:0.056:1561:0|1:16894472_A_G | |
| chr1 16894523 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=4909;ECNT=3;FS=0;HCNT=4;MAX_ED=51;MIN_ED=4;MQ=43;MQ0=738;MQRankSum=-1.928;NLOD=172.57;ReadPosRankSum=0.695;TLOD=15.63;ANN=A|missense_variant&splice_region_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|24/29|c.2617C>T|p.His873Tyr|3505/5932|2617/3420|873/1139||,A|missense_variant&splice_region_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|7/9|c.827C>T|p.Thr276Ile|827/1069|827/900|276/299||,A|splice_region_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/19|c.*1485C>T||||||,A|splice_region_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/6|c.*169C>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|15/19|c.*1485C>T|||||14690|,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|4/6|c.*169C>T|||||5116|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.*6460C>T|||||1060|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:2478,44:0.017:2522 0/0:1332,46:0.039:1378 | |
| chr1 16895695 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1863;ECNT=2;FS=7.297;HCNT=12;MAX_ED=57;MIN_ED=57;MQ=38.32;MQ0=453;MQRankSum=0.403;NLOD=57.03;ReadPosRankSum=4.448;TLOD=5.91;ANN=T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|23/29|c.2487G>A|p.Gln829Gln|3375/5932|2487/3420|829/1139||,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|14/19|c.*1355G>A|||||13518|,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|3/6|c.*39G>A|||||3944|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|5/5|c.*90G>A|||||5288|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|6/8|c.825-1170G>A|||||| GT:AD:AF:DP 0/1:729,19:0.018:748 0/0:517,27:0.039:544 | |
| chr1 16895752 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1552;ECNT=2;FS=1.947;HCNT=5;MAX_ED=57;MIN_ED=57;MQ=36.1;MQ0=476;MQRankSum=0.657;NLOD=59.94;ReadPosRankSum=0.468;TLOD=10.69;ANN=C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|22/28|c.2451-21C>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|13/18|c.*1319-21C>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|2/5|c.*3-21C>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|6/8|c.825-1227C>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|4/4|c.*54-21C>G||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:512,10:0.012:522 0/0:433,15:0.027:448 | |
| chr1 16901021 . A G . PASS ClippingRankSum=0;DP=3198;ECNT=1;FS=0;HCNT=27;MAX_ED=.;MIN_ED=.;MQ=36.62;MQ0=807;MQRankSum=1.196;NLOD=17.09;ReadPosRankSum=-0.313;TLOD=70.21;ANN=G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|21/29|c.2359T>C|p.Ser787Pro|3247/5932|2359/3420|787/1139||,G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding|1/6|c.13T>C|p.Ser5Pro|31/531|13/102|5/33||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|5/9|c.733T>C|p.Ser245Pro|733/1069|733/900|245/299||,G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|3/5|c.454T>C|p.Ser152Pro|454/694|454/492|152/163||WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|12/19|c.*1227T>C|||||8192| GT:AD:AF:DP 0/1:1227,109:0.059:1336 0/0:813,99:0.094:912 | |
| chr1 16902844 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2195;ECNT=4;FS=0;HCNT=14;MAX_ED=144;MIN_ED=12;MQ=45.62;MQ0=137;MQRankSum=0.605;NLOD=30.50;ReadPosRankSum=2.71;TLOD=74.60;ANN=T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|19/29|c.2037C>A|p.Asp679Glu|2925/5932|2037/3420|679/1139||,T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|3/9|c.411C>A|p.Asp137Glu|411/1069|411/900|137/299||,T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|1/5|c.132C>A|p.Asp44Glu|132/694|132/492|44/163||WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|10/19|c.*905C>A|||||6369|,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-1811C>A|||||1793|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:1230,81:0.052:1311 0/0:567,46:0.062:613 | |
| chr1 16902856 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2155;ECNT=4;FS=1.137;HCNT=16;MAX_ED=144;MIN_ED=12;MQ=45.19;MQ0=149;MQRankSum=-1.056;NLOD=59.26;ReadPosRankSum=1.763;TLOD=89.14;ANN=T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|19/29|c.2025G>A|p.Pro675Pro|2913/5932|2025/3420|675/1139||,T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|3/9|c.399G>A|p.Pro133Pro|399/1069|399/900|133/299||,T|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|1/5|c.120G>A|p.Pro40Pro|120/694|120/492|40/163||WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|10/19|c.*893G>A|||||6357|,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-1823G>A|||||1805|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:1177,92:0.07:1269 0/0:560,32:0.051:592 | |
| chr1 16902931 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2123;ECNT=4;FS=1.833;HCNT=4;MAX_ED=144;MIN_ED=12;MQ=41.35;MQ0=221;MQRankSum=1.513;NLOD=95.12;ReadPosRankSum=-4.042;TLOD=21.65;ANN=G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|19/29|c.1950G>C|p.Gln650His|2838/5932|1950/3420|650/1139||,G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|3/9|c.324G>C|p.Gln108His|324/1069|324/900|108/299||,G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding|1/5|c.45G>C|p.Gln15His|45/694|45/492|15/163||WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|10/19|c.*818G>C|||||6282|,G|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-1898G>C|||||1880|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:1042,28:0.021:1070 0/0:593,21:0.024:614 | |
| chr1 16902988 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2410;ECNT=4;FS=9.949;HCNT=11;MAX_ED=144;MIN_ED=12;MQ=45.2;MQ0=137;MQRankSum=-7.299;NLOD=73.61;ReadPosRankSum=0.096;TLOD=87.74;ANN=T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-1955G>A|||||1937|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-13G>A|||||13|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|18/28|c.1905-12G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|9/18|c.*773-12G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|2/8|c.279-12G>A|||||| GT:AD:AF:DP 0/1:1217,85:0.072:1302 0/0:674,30:0.049:704 | |
| chr1 16903776 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=852;ECNT=4;FS=1.12;HCNT=5;MAX_ED=196;MIN_ED=5;MQ=51.56;MQ0=23;MQRankSum=-3.788;NLOD=5.89;ReadPosRankSum=3.476;TLOD=59.36;ANN=G|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-2743G>C|||||2725|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-801G>C|||||801|WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|18/28|c.1904+36G>C||||||,G|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|9/18|c.*772+36G>C||||||,G|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|2/8|c.278+36G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:481,33:0.058:514:0|1:16903776_C_G 0/0:241,19:0.073:260:0|1:16903776_C_G | |
| chr1 16903781 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=855;ECNT=4;FS=0;HCNT=5;MAX_ED=196;MIN_ED=5;MQ=51.47;MQ0=25;MQRankSum=-3.398;NLOD=7.39;ReadPosRankSum=3.554;TLOD=59.04;ANN=T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-2748G>A|||||2730|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-806G>A|||||806|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|18/28|c.1904+31G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|9/18|c.*772+31G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|2/8|c.278+31G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:480,31:0.056:511:0|1:16903776_C_G 0/0:243,19:0.071:262:0|1:16903776_C_G | |
| chr1 16903786 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=860;ECNT=4;FS=1.204;HCNT=5;MAX_ED=196;MIN_ED=5;MQ=51.26;MQ0=27;MQRankSum=-3.155;NLOD=5.89;ReadPosRankSum=3.068;TLOD=59.16;ANN=C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-2753A>G|||||2735|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-811A>G|||||811|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|18/28|c.1904+26A>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|9/18|c.*772+26A>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|2/8|c.278+26A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:482,30:0.055:512:0|1:16903776_C_G 0/0:241,19:0.073:260:0|1:16903776_C_G | |
| chr1 16903972 . T C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=284;ECNT=4;FS=22.434;HCNT=6;MAX_ED=196;MIN_ED=5;MQ=42.3;MQ0=37;MQRankSum=-3.665;NLOD=19.26;ReadPosRankSum=-0.087;TLOD=6.55;ANN=C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420031|protein_coding||c.-2939A>G|||||2921|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-997A>G|||||997|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|17/28|c.1802-58A>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|8/18|c.*670-58A>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding|1/8|c.176-58A>G|||||| GT:AD:AF:DP 0/1:127,6:0.053:133 0/0:93,0:0:93 | |
| chr1 16907279 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=3021;ECNT=4;FS=3.004;HCNT=3;MAX_ED=62;MIN_ED=24;MQ=54.07;MQ0=72;MQRankSum=-3.071;NLOD=172.49;ReadPosRankSum=-4.876;TLOD=13.75;ANN=C|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|16/29|c.1552T>G|p.Ser518Ala|2440/5932|1552/3420|518/1139||,C|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|7/19|c.*420T>G|||||1934|,C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-1417T>G|||||1417|,C|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-4304T>G|||||4304|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:2007,18:0.013:2025 0/0:892,18:0.02:910 | |
| chr1 16907303 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=3138;ECNT=4;FS=1.404;HCNT=8;MAX_ED=62;MIN_ED=24;MQ=52.92;MQ0=78;MQRankSum=-9.715;NLOD=92.67;ReadPosRankSum=-1.243;TLOD=174.72;ANN=T|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|16/29|c.1528G>A|p.Ala510Thr|2416/5932|1528/3420|510/1139||,T|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|7/19|c.*396G>A|||||1910|,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-1441G>A|||||1441|,T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-4328G>A|||||4328|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:2024,88:0.063:2112 0/0:875,48:0.059:923 | |
| chr1 16907307 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=3146;ECNT=4;FS=3.027;HCNT=3;MAX_ED=62;MIN_ED=24;MQ=52.63;MQ0=78;MQRankSum=-3.984;NLOD=153.30;ReadPosRankSum=-1.132;TLOD=54.44;ANN=A|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|16/29|c.1524C>T|p.Asn508Asn|2412/5932|1524/3420|508/1139||,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|7/19|c.*392C>T|||||1906|,A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-1445C>T|||||1445|,A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-4332C>T|||||4332|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:2084,31:0.017:2115 0/0:903,25:0.027:928 | |
| chr1 16907341 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=3135;ECNT=4;FS=0;HCNT=3;MAX_ED=62;MIN_ED=24;MQ=51.27;MQ0=84;MQRankSum=1.851;NLOD=20.77;ReadPosRankSum=0.617;TLOD=75.99;ANN=A|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|16/29|c.1490A>T|p.Asn497Ile|2378/5932|1490/3420|497/1139||,A|3_prime_UTR_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|7/19|c.*358A>T|||||1872|,A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-1479A>T|||||1479|,A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-4366A>T|||||4366|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:2054,76:0.033:2130 0/0:822,62:0.077:884 | |
| chr1 16907855 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2080;ECNT=2;FS=5.184;HCNT=5;MAX_ED=172;MIN_ED=172;MQ=50.64;MQ0=278;MQRankSum=-2.186;NLOD=9.53;ReadPosRankSum=1.297;TLOD=88.07;ANN=A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-1993C>T|||||1993|,A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000287968|protein_coding||c.-4880C>T|||||4880|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|15/28|c.1379+60C>T||||||,A|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|6/18|c.*247+60C>T|||||| GT:AD:AF:DP 0/1:1154,75:0.065:1229 0/0:441,83:0.137:524 | |
| chr1 16908027 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1746;ECNT=2;FS=25.61;HCNT=4;MAX_ED=172;MIN_ED=172;MQ=57.69;MQ0=35;MQRankSum=-16.524;NLOD=52.49;ReadPosRankSum=-1.991;TLOD=59.18;ANN=A|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-2165G>T|||||2165|,A|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|14/28|c.1307-40G>T||||||,A|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|5/18|c.*175-40G>T|||||| GT:AD:AF:DP 0/1:1159,42:0.05:1201 0/0:480,18:0.051:498 | |
| chr1 16910063 . C T . PASS ClippingRankSum=0;DP=769;ECNT=1;FS=17.088;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=47.14;MQ0=109;MQRankSum=-6.421;NLOD=6.46;ReadPosRankSum=-1.188;TLOD=51.99;ANN=T|upstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000432949|protein_coding||c.-4201G>A|||||4201|,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|13/28|c.1091+26G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.176-810G>A|||||| GT:AD:AF:DP 0/1:342,33:0.117:375 0/0:225,16:0.083:241 | |
| chr1 16916380 . T C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=593;ECNT=6;FS=6.311;HCNT=6;MAX_ED=136;MIN_ED=86;MQ=46.24;MQ0=144;MQRankSum=-1.411;NLOD=26.73;ReadPosRankSum=-1.024;TLOD=4.93;ANN=C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3677A>G|||||3677|,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|8/28|c.278+14A>G||||||,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1962A>G|||||| GT:AD:AF:DP 0/1:256,7:0.027:263 0/0:160,0:0:160 | |
| chr1 16916466 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=483;ECNT=6;FS=67.058;HCNT=16;MAX_ED=136;MIN_ED=86;MQ=44.49;MQ0=69;MQRankSum=-2.324;NLOD=13.11;ReadPosRankSum=-4.981;TLOD=43.06;ANN=G|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|8/29|c.206T>C|p.Phe69Ser|1094/5932|206/3420|69/1139||,G|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3591T>C|||||3591|,G|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1876T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:211,18:0.089:229:0|1:16916466_A_G 0/0:141,5:0.043:146:0|1:16916466_A_G | |
| chr1 16916476 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=498;ECNT=6;FS=9.145;HCNT=9;MAX_ED=136;MIN_ED=86;MQ=44.69;MQ0=68;MQRankSum=-2.622;NLOD=25.94;ReadPosRankSum=0.495;TLOD=9.37;ANN=C|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|8/29|c.196C>G|p.Leu66Val|1084/5932|196/3420|66/1139||,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3581C>G|||||3581|,C|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1866C>G|||||| GT:AD:AF:DP 0/1:223,8:0.037:231 0/0:150,3:0.017:153 | |
| chr1 16916483 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=502;ECNT=6;FS=33.258;HCNT=16;MAX_ED=136;MIN_ED=86;MQ=44.94;MQ0=65;MQRankSum=-2.949;NLOD=25.34;ReadPosRankSum=-4.016;TLOD=26.16;ANN=G|synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|8/29|c.189T>C|p.Cys63Cys|1077/5932|189/3420|63/1139||,G|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3574T>C|||||3574|,G|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1859T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:224,8:0.051:232:0|1:16916466_A_G 0/0:155,1:0.016:156:0|1:16916466_A_G | |
| chr1 16916495 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=512;ECNT=6;FS=10.533;HCNT=16;MAX_ED=136;MIN_ED=86;MQ=45.04;MQ0=63;MQRankSum=-1.255;NLOD=28.01;ReadPosRankSum=-2.497;TLOD=4.19;ANN=T|splice_region_variant&synonymous_variant|LOW|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|8/29|c.177G>A|p.Lys59Lys|1065/5932|177/3420|59/1139||,T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3562G>A|||||3562|,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1847G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:235,2:0.011:237:0|1:16916466_A_G 0/0:158,1:0.008403:159:0|1:16916466_A_G | |
| chr1 16916516 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=520;ECNT=6;FS=14.634;HCNT=14;MAX_ED=136;MIN_ED=86;MQ=45.14;MQ0=60;MQRankSum=-3.861;NLOD=18.29;ReadPosRankSum=0.263;TLOD=42.04;ANN=T|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*3541G>A|||||3541|,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|7/28|c.176-20G>A||||||,T|intron_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/18|c.175+1826G>A|||||| GT:AD:AF:DP 0/1:222,29:0.119:251 0/0:150,6:0.035:156 | |
| chr1 16918424 . G C . PASS ClippingRankSum=0;DP=2310;ECNT=1;FS=0.984;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=57.13;MQ0=25;MQRankSum=-27.183;NLOD=11.76;ReadPosRankSum=-0.629;TLOD=221.64;ANN=C|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000430580|protein_coding|7/29|c.93C>G|p.Asn31Lys|981/5932|93/3420|31/1139||,C|missense_variant|MODERATE|NBPF1|ENSG00000219481|transcript|ENST00000392963|nonsense_mediated_decay|4/19|c.93C>G|p.Asn31Lys|551/2672|93/216|31/71||,C|downstream_gene_variant|MODIFIER|NBPF1|ENSG00000219481|transcript|ENST00000420513|processed_transcript||n.*1633C>G|||||1633| GT:AD:AF:DP 0/1:1414,145:0.108:1559 0/0:640,46:0.081:686 | |
| chr1 16945452 . C T . t_lod_fstar ClippingRankSum=0;DP=151;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=59.89;MQ0=0;MQRankSum=-3.93;NLOD=2.51;ReadPosRankSum=0.623;TLOD=4.63;ANN=T|downstream_gene_variant|MODIFIER|RP5-1182A14.5|ENSG00000271732|transcript|ENST00000607700|lincRNA||n.*1228C>T|||||1228|,T|non_coding_transcript_exon_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000412962|lincRNA|8/8|n.2068G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000540383|lincRNA|7/7|n.1064G>A|||||| GT:AD:AF:DP 0/1:99,6:0.065:105 0/0:42,3:0.091:45 | |
| chr1 16952267 . T C . PASS ClippingRankSum=0;DP=114;ECNT=1;FS=2.029;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.65;ReadPosRankSum=-0.144;TLOD=29.25;ANN=C|splice_region_variant&intron_variant|LOW|CROCCP2|ENSG00000215908|transcript|ENST00000412962|lincRNA|7/7|n.1000+3A>G||||||,C|splice_region_variant&intron_variant|LOW|CROCCP2|ENSG00000215908|transcript|ENST00000540383|lincRNA|5/6|n.723+3A>G||||||,C|downstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.*3898A>G|||||3898| GT:AD:AF:DP 0/1:64,18:0.236:82 0/0:30,2:0.042:32 | |
| chr1 16952896 . G A . PASS ClippingRankSum=0;DP=190;ECNT=1;FS=3.73;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=59.79;MQ0=0;MQRankSum=-0.079;NLOD=2.75;ReadPosRankSum=-0.238;TLOD=36.50;ANN=A|downstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.*3269C>T|||||3269|,A|non_coding_transcript_exon_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000412962|lincRNA|6/8|n.721C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000540383|lincRNA|4/7|n.444C>T|||||| GT:AD:AF:DP 0/1:98,23:0.205:121 0/0:63,6:0.07:69 | |
| chr1 16956555 . C T . PASS ClippingRankSum=0;DP=350;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=59.93;MQ0=0;MQRankSum=0.343;NLOD=7.44;ReadPosRankSum=-0.059;TLOD=38.82;ANN=T|intron_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000412962|lincRNA|3/7|n.294+830G>A||||||,T|intron_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000540383|lincRNA|1/6|n.17+830G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron|6/6|n.1639G>A|||||| GT:AD:AF:DP 0/1:212,31:0.119:243 0/0:102,4:0.057:106 | |
| chr1 16965863 . ACAG A . germline_risk ClippingRankSum=0;DP=199;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=59.53;MQ0=2;MQRankSum=-4.107;NLOD=2.03;ReadPosRankSum=-0.205;TLOD=10.66;ANN=A|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000412962|lincRNA||n.-4812_-4810delCTG|||||4810|,A|intron_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron|2/5|n.156+3657_156+3659delCTG|||||| GT:AD:AF:DP 0/1:102,4:0.051:106 0/0:43,4:0.056:47 | |
| chr1 16973327 . G A . t_lod_fstar ClippingRankSum=0;DP=283;ECNT=1;FS=0.962;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=43.76;MQ0=84;MQRankSum=-2.181;NLOD=7.54;ReadPosRankSum=1.061;TLOD=5.88;ANN=A|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-2149C>T|||||2149|,A|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|3/6|n.326+123G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|5/20|n.407G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|4/18|n.363G>A|||||| GT:AD:AF:DP 0/1:78,8:0.072:86 0/0:88,9:0.099:97 | |
| chr1 16973423 . C T . PASS ClippingRankSum=0;DP=372;ECNT=1;FS=0.97;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=47.46;MQ0=72;MQRankSum=-2.31;NLOD=8.64;ReadPosRankSum=0.269;TLOD=18.04;ANN=T|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-2245G>A|||||2245|,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|5/19|n.476+27C>T||||||,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|3/6|n.327-52C>T||||||,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|4/17|n.432+27C>T|||||| GT:AD:AF:DP 0/1:147,11:0.082:158 0/0:125,8:0.065:133 | |
| chr1 16973519 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=695;ECNT=2;FS=3.064;HCNT=7;MAX_ED=129;MIN_ED=129;MQ=47.57;MQ0=56;MQRankSum=-0.544;NLOD=10.54;ReadPosRankSum=1.471;TLOD=22.77;ANN=A|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-2341C>T|||||2341|,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|6/20|n.521G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|4/7|n.371G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|5/18|n.477G>A|||||| GT:AD:AF:DP 0/1:385,20:0.05:405 0/0:202,11:0.067:213 | |
| chr1 16973648 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=931;ECNT=2;FS=9.121;HCNT=4;MAX_ED=129;MIN_ED=129;MQ=54.32;MQ0=22;MQRankSum=-2.682;NLOD=49.93;ReadPosRankSum=-0.118;TLOD=13.64;ANN=G|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-2470T>C|||||2470|,G|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|6/19|n.613+37A>G||||||,G|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|4/6|n.463+37A>G||||||,G|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|5/17|n.569+37A>G|||||| GT:AD:AF:DP 0/1:593,12:0.028:605 0/0:281,12:0.046:293 | |
| chr1 16974312 . G C . PASS ClippingRankSum=0;DP=474;ECNT=1;FS=10.785;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=53.5;MQ0=9;MQRankSum=-2.386;NLOD=17.84;ReadPosRankSum=-1.244;TLOD=13.75;ANN=C|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-3134C>G|||||3134|,C|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|9/20|n.887G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|7/7|n.733G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|8/18|n.843G>C|||||| GT:AD:AF:DP 0/1:281,9:0.048:290 0/0:152,7:0.057:159 | |
| chr1 16974549 . C G . PASS ClippingRankSum=0;DP=588;ECNT=1;FS=13.954;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=57.11;MQ0=2;MQRankSum=-8.16;NLOD=20.46;ReadPosRankSum=-4.921;TLOD=34.44;ANN=G|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-3371G>C|||||3371|,G|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|9/19|n.1023-14C>G||||||,G|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|8/17|n.979-14C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene|7/7|n.970C>G|||||| GT:AD:AF:DP 0/1:356,22:0.069:378 0/0:188,8:0.058:196 | |
| chr1 16974901 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=180;ECNT=3;FS=10.853;HCNT=12;MAX_ED=71;MIN_ED=14;MQ=57.92;MQ0=5;MQRankSum=-10.534;NLOD=3.57;ReadPosRankSum=-2.293;TLOD=9.29;ANN=G|splice_region_variant&intron_variant|LOW|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|11/19|n.1256+5A>G||||||,G|splice_region_variant&intron_variant|LOW|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|10/17|n.1212+5A>G||||||,G|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-3723T>C|||||3723|,G|downstream_gene_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene||n.*30A>G|||||30| GT:AD:AF:DP 0/1:109,4:0.052:113 0/0:55,2:0.051:57 | |
| chr1 16974915 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=191;ECNT=3;FS=16.533;HCNT=12;MAX_ED=71;MIN_ED=14;MQ=58.04;MQ0=5;MQRankSum=-10.041;NLOD=4.71;ReadPosRankSum=-2.076;TLOD=9.22;ANN=T|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-3737G>A|||||3737|,T|downstream_gene_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene||n.*44C>T|||||44|,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|11/19|n.1256+19C>T||||||,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|10/17|n.1213-12C>T|||||| GT:AD:AF:DP 0/1:116,4:0.05:120 0/0:58,3:0.07:61 | |
| chr1 16974972 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=247;ECNT=3;FS=8.549;HCNT=11;MAX_ED=71;MIN_ED=14;MQ=56.9;MQ0=10;MQRankSum=-12.549;NLOD=4.87;ReadPosRankSum=0.744;TLOD=16.25;ANN=T|upstream_gene_variant|MODIFIER|CROCCP2|ENSG00000215908|transcript|ENST00000362058|retained_intron||n.-3794G>A|||||3794|,T|downstream_gene_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene||n.*101C>T|||||101|,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|11/19|n.1257-52C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|11/18|n.1258C>T|||||| GT:AD:AF:DP 0/1:137,13:0.089:150 0/0:73,4:0.054:77 | |
| chr1 16976392 . G A . t_lod_fstar ClippingRankSum=0;DP=205;ECNT=1;FS=0;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=43.08;MQ0=15;MQRankSum=-0.927;NLOD=11.72;ReadPosRankSum=-1.959;TLOD=4.28;ANN=A|downstream_gene_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene||n.*1521G>A|||||1521|,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|19/20|n.1970G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|17/18|n.2023G>A|||||| GT:AD:AF:DP 0/1:104,4:0.037:108 0/0:58,0:0:58 | |
| chr1 16976528 . G T . PASS ClippingRankSum=0;DP=594;ECNT=1;FS=0;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=47.36;MQ0=59;MQRankSum=-5.76;NLOD=14.25;ReadPosRankSum=0.483;TLOD=75.03;ANN=T|downstream_gene_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000418421|unprocessed_pseudogene||n.*1657G>T|||||1657|,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000334429|unprocessed_pseudogene|19/19|n.2023-41G>T||||||,T|intron_variant|MODIFIER|MST1P2|ENSG00000186301|transcript|ENST00000457982|unprocessed_pseudogene|17/17|n.2076-41G>T|||||| GT:AD:AF:DP 0/1:261,47:0.164:308 0/0:164,17:0.084:181 | |
| chr1 17007589 . G A . germline_risk ClippingRankSum=0;DP=1986;ECNT=1;FS=8.051;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=36.49;MQ0=674;MQRankSum=0.004;NLOD=1.98;ReadPosRankSum=-2.567;TLOD=30.59;ANN=A|upstream_gene_variant|MODIFIER|AL021920.1|ENSG00000264742|transcript|ENST00000584111|miRNA||n.-161G>A|||||161|,A|downstream_gene_variant|MODIFIER|EIF1AXP1|ENSG00000236698|transcript|ENST00000419267|processed_pseudogene||n.*4527C>T|||||4527|,A|intergenic_region|MODIFIER|FAM231A-AL021920.1|ENSG00000237847-ENSG00000264742|intergenic_region|ENSG00000237847-ENSG00000264742|||n.17007589G>A|||||| GT:AD:AF:DP 0/1:703,25:0.047:728 0/0:483,31:0.077:514 | |
| chr1 17019567 . G A . germline_risk ClippingRankSum=0;DP=19;ECNT=1;FS=0;HCNT=40;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.80;ReadPosRankSum=-1.811;TLOD=8.42;ANN=A|upstream_gene_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000414828|processed_transcript||n.-763C>T|||||763|,A|intron_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000270691|transcribed_unprocessed_pseudogene|10/10|n.1939-1778C>T||||||,A|intron_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000492551|processed_transcript|10/10|n.1939-1778C>T|||||| GT:AD:AF:DP 0/1:8,5:0.4:13 0/0:6,0:0:6 | |
| chr1 17020211 . C A . PASS ClippingRankSum=0;DP=56;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.56;ReadPosRankSum=-0.664;TLOD=14.08;ANN=A|upstream_gene_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000414828|processed_transcript||n.-1407G>T|||||1407|,A|intron_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000270691|transcribed_unprocessed_pseudogene|10/10|n.1939-2422G>T||||||,A|intron_variant|MODIFIER|ESPNP|ENSG00000268869|transcript|ENST00000492551|processed_transcript|10/10|n.1939-2422G>T|||||| GT:AD:AF:DP 0/1:30,10:0.226:40 0/0:16,0:0:16 | |
| chr1 17084415 . T C . germline_risk ClippingRankSum=0;DP=178;ECNT=1;FS=12.909;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=58.27;MQ0=1;MQRankSum=-6.537;NLOD=1.61;ReadPosRankSum=-2.643;TLOD=9.02;ANN=C|downstream_gene_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000544155|processed_transcript||n.*133A>G|||||133|,C|downstream_gene_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000545160|processed_transcript||n.*2917A>G|||||2917|,C|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000389184|transcribed_unprocessed_pseudogene|17/19|n.1646+22A>G||||||,C|intron_variant|MODIFIER|CROCC|ENSG00000058453|transcript|ENST00000466256|processed_transcript|1/8|n.125+17523T>C||||||,C|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000455405|processed_transcript|5/7|n.453+22A>G||||||,C|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000442552|transcribed_unprocessed_pseudogene|14/16|n.1776+22A>G|||||| GT:AD:AF:DP 0/1:114,7:0.069:121 0/0:46,7:0.136:53 | |
| chr1 17084626 . G A . germline_risk;t_lod_fstar ClippingRankSum=0;DP=167;ECNT=1;FS=9.33;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=43.05;MQ0=12;MQRankSum=-0.22;NLOD=1.96;ReadPosRankSum=-2.566;TLOD=6.02;ANN=A|downstream_gene_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000545160|processed_transcript||n.*2706C>T|||||2706|,A|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000389184|transcribed_unprocessed_pseudogene|16/19|n.1500-43C>T||||||,A|intron_variant|MODIFIER|CROCC|ENSG00000058453|transcript|ENST00000466256|processed_transcript|1/8|n.125+17734G>A||||||,A|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000455405|processed_transcript|4/7|n.307-43C>T||||||,A|intron_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000442552|transcribed_unprocessed_pseudogene|13/16|n.1630-43C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|MST1L|ENSG00000186715|transcript|ENST00000544155|processed_transcript|3/3|n.514C>T|||||| GT:AD:AF:DP 0/1:104,4:0.056:108 0/0:38,3:0.091:41 | |
| chr1 17185415 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=366;ECNT=2;FS=17.657;HCNT=5;MAX_ED=7;MIN_ED=7;MQ=52.83;MQ0=2;MQRankSum=-3.398;NLOD=6.11;ReadPosRankSum=-0.322;TLOD=34.65;ANN=G|downstream_gene_variant|MODIFIER|MIR3675|ENSG00000263811|transcript|ENST00000583661|miRNA||n.*29G>C|||||29|,G|intron_variant|MODIFIER|RP11-108M9.2|ENSG00000230239|transcript|ENST00000414128|lincRNA|2/2|n.647-129C>G||||||,G|intron_variant|MODIFIER|CROCC|ENSG00000058453|transcript|ENST00000466256|processed_transcript|1/8|n.126-71366C>G|||||| GT:AD:AF:DP:PGT:PID 0/1:205,12:0.064:217:0|1:17185415_C_G 0/0:116,6:0.055:122:0|1:17185415_C_G | |
| chr1 17185422 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=421;ECNT=2;FS=22.007;HCNT=5;MAX_ED=7;MIN_ED=7;MQ=52.32;MQ0=2;MQRankSum=-3.837;NLOD=5.30;ReadPosRankSum=-0.515;TLOD=39.56;ANN=G|downstream_gene_variant|MODIFIER|MIR3675|ENSG00000263811|transcript|ENST00000583661|miRNA||n.*22T>C|||||22|,G|intron_variant|MODIFIER|RP11-108M9.2|ENSG00000230239|transcript|ENST00000414128|lincRNA|2/2|n.647-122A>G||||||,G|intron_variant|MODIFIER|CROCC|ENSG00000058453|transcript|ENST00000466256|processed_transcript|1/8|n.126-71359A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:235,15:0.068:250:0|1:17185415_C_G 0/0:130,7:0.059:137:0|1:17185415_C_G | |
| chr1 17197637 . A G . PASS ClippingRankSum=0;DP=235;ECNT=1;FS=6.838;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=54.78;MQ0=2;MQRankSum=-4.042;NLOD=2.86;ReadPosRankSum=1.833;TLOD=10.23;ANN=G|upstream_gene_variant|MODIFIER|U1|ENSG00000228549|transcript|ENST00000451828|lincRNA||n.-1116A>G|||||1116|,G|upstream_gene_variant|MODIFIER|U1|ENSG00000228549|transcript|ENST00000453554|lincRNA||n.-1142A>G|||||1142|,G|upstream_gene_variant|MODIFIER|U1|ENSG00000228549|transcript|ENST00000457856|lincRNA||n.-1897A>G|||||1897|,G|upstream_gene_variant|MODIFIER|U1|ENSG00000228549|transcript|ENST00000362684|snRNA||n.-2566A>G|||||2566|,G|intron_variant|MODIFIER|CROCC|ENSG00000058453|transcript|ENST00000466256|processed_transcript|1/8|n.126-59144A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|U1|ENSG00000228549|transcript|ENST00000438002|lincRNA|1/2|n.198A>G|||||| GT:AD:AF:DP 0/1:150,12:0.063:162 0/0:60,4:0.067:64 | |
| chr1 17660890 . C A . germline_risk ClippingRankSum=0;DP=38;ECNT=1;FS=4.728;HCNT=15;MAX_ED=.;MIN_ED=.;MQ=59.92;MQ0=0;MQRankSum=-0.709;NLOD=1.76;ReadPosRankSum=1.129;TLOD=75.75;ANN=A|3_prime_UTR_variant|MODIFIER|PADI4|ENSG00000159339|transcript|ENST00000375453|protein_coding|4/4|c.*28C>A|||||28|,A|intron_variant|MODIFIER|PADI4|ENSG00000159339|transcript|ENST00000375448|protein_coding|3/15|c.340+386C>A||||||,A|intron_variant|MODIFIER|AC004824.2|ENSG00000269468|transcript|ENST00000602074|protein_coding|4/5|c.223-2671G>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:7,24:0.793:31 0/0:7,0:0:7 | |
| chr1 17928600 . C T . PASS ClippingRankSum=0;DP=135;ECNT=1;FS=0.76;HCNT=33;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.99;ReadPosRankSum=0.38;TLOD=72.09;ANN=T|upstream_gene_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000482892|processed_transcript||n.-66C>T|||||66|,T|intron_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000361221|protein_coding|4/28|c.258-22C>T||||||,T|intron_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000434513|protein_coding|4/26|c.258-22C>T||||||,T|intron_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000452522|protein_coding|4/27|c.258-22C>T||||||,T|intron_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000375415|protein_coding|3/26|c.258-22C>T||||||,T|intron_variant|MODIFIER|ARHGEF10L|ENSG00000074964|transcript|ENST00000375420|protein_coding|1/16|c.-352-22C>T|||||| GT:AD:AF:DP 0/1:46,36:0.46:82 0/0:52,0:0:52 | |
| chr1 20978904 . A G . t_lod_fstar ClippingRankSum=0;DP=37;ECNT=1;FS=2.191;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.41;ReadPosRankSum=0;TLOD=4.09;ANN=G|synonymous_variant|LOW|DDOST|ENSG00000244038|transcript|ENST00000375048|protein_coding|11/11|c.1339T>C|p.Leu447Leu|1445/2079|1339/1371|447/456||,G|synonymous_variant|LOW|DDOST|ENSG00000244038|transcript|ENST00000602624|protein_coding|11/11|c.1288T>C|p.Leu430Leu|1329/1963|1288/1320|430/439||,G|synonymous_variant|LOW|DDOST|ENSG00000244038|transcript|ENST00000415136|protein_coding|10/10|c.1228T>C|p.Leu410Leu|1232/1589|1228/1260|410/419||,G|upstream_gene_variant|MODIFIER|PINK1-AS|ENSG00000117242|transcript|ENST00000451424|retained_intron||n.-218T>C|||||218|,G|upstream_gene_variant|MODIFIER|AL391357.1|ENSG00000257033|transcript|ENST00000535128|pseudogene||n.-1697T>C|||||1697|,G|downstream_gene_variant|MODIFIER|PINK1|ENSG00000158828|transcript|ENST00000321556|protein_coding||c.*1720A>G|||||900|,G|downstream_gene_variant|MODIFIER|PINK1|ENSG00000158828|transcript|ENST00000492302|processed_transcript||n.*1095A>G|||||1095|,G|downstream_gene_variant|MODIFIER|PINK1|ENSG00000158828|transcript|ENST00000400490|processed_transcript||n.*901A>G|||||901|,G|downstream_gene_variant|MODIFIER|DDOST|ENSG00000244038|transcript|ENST00000475210|processed_transcript||n.*223T>C|||||223|,G|downstream_gene_variant|MODIFIER|DDOST|ENSG00000244038|transcript|ENST00000464364|protein_coding||c.*3029T>C|||||3029|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:24,3:0.095:27 0/0:10,0:0:10 | |
| chr1 21054029 . AGCT A . t_lod_fstar ClippingRankSum=0;DP=121;ECNT=1;FS=2.946;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=-0.136;TLOD=5.24;ANN=A|disruptive_inframe_deletion|MODERATE|SH2D5|ENSG00000189410|transcript|ENST00000444387|protein_coding|3/10|c.152_154delAGC|p.Gln51del|552/1934|152/1272|51/423||,A|disruptive_inframe_deletion|MODERATE|SH2D5|ENSG00000189410|transcript|ENST00000447746|protein_coding|3/5|c.152_154delAGC|p.Gln51del|294/544|152/404|51/133||WARNING_TRANSCRIPT_INCOMPLETE,A|disruptive_inframe_deletion|MODERATE|SH2D5|ENSG00000189410|transcript|ENST00000518294|protein_coding|3/6|c.152_154delAGC|p.Gln51del|270/511|152/395|51/130||WARNING_TRANSCRIPT_INCOMPLETE,A|disruptive_inframe_deletion|MODERATE|SH2D5|ENSG00000189410|transcript|ENST00000517430|protein_coding|3/5|c.152_154delAGC|p.Gln51del|340/564|152/378|51/125||WARNING_TRANSCRIPT_NO_STOP_CODON,A|disruptive_inframe_deletion|MODERATE|SH2D5|ENSG00000189410|transcript|ENST00000519434|protein_coding|4/5|c.152_154delAGC|p.Gln51del|466/524|152/212|51/69||WARNING_TRANSCRIPT_INCOMPLETE,A|5_prime_UTR_variant|MODIFIER|SH2D5|ENSG00000189410|transcript|ENST00000375031|protein_coding|2/9|c.-101_-99delAGC|||||1480|,A|intron_variant|MODIFIER|SH2D5|ENSG00000189410|transcript|ENST00000460804|processed_transcript|1/5|n.75-2904_75-2902delAGC|||||| GT:AD:AF:DP 0/1:86,2:0.035:88 0/0:30,0:0:30 | |
| chr1 21267707 . GCAA G . PASS ClippingRankSum=0;DP=115;ECNT=1;FS=0;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=0.484;TLOD=8.22;ANN=G|downstream_gene_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000356916|protein_coding||c.*159_*161delTTG|||||27|,G|downstream_gene_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000374927|protein_coding||c.*159_*161delTTG|||||32|,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000374937|protein_coding|9/31|c.1513+274_1513+276delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000264211|protein_coding|8/30|c.1495+274_1495+276delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000400422|protein_coding|11/33|c.1495+274_1495+276delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000602326|protein_coding|12/34|c.1513+274_1513+276delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000374935|protein_coding|7/29|c.655+8786_655+8788delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000536266|protein_coding|3/25|c.307+274_307+276delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000374933|processed_transcript|1/4|n.140+42_140+44delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000544689|protein_coding|2/5|c.124+42_124+44delTTG||||||,G|intron_variant|MODIFIER|EIF4G3|ENSG00000075151|transcript|ENST00000485722|processed_transcript|1/1|n.226+42_226+44delTTG|||||| GT:AD:AF:DP 0/1:79,4:0.046:83 0/0:30,0:0:30 | |
| chr1 22174426 . T G . germline_risk ClippingRankSum=0;DP=24;ECNT=1;FS=4.481;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.50;ReadPosRankSum=-0.551;TLOD=42.14;ANN=G|missense_variant|MODERATE|HSPG2|ENSG00000142798|transcript|ENST00000453796|protein_coding|1/4|c.26A>C|p.Tyr9Ser|26/621|26/621|9/206||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000493940|processed_transcript||n.*3378A>C|||||3378|,G|intron_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000374695|protein_coding|60/96|c.7873+25A>C||||||,G|intron_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000430507|protein_coding|15/18|c.*1222+25A>C||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:3,15:0.867:18 0/0:6,0:0:6 | |
| chr1 22195995 . AGAG A . t_lod_fstar ClippingRankSum=0;DP=42;ECNT=1;FS=0;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.71;ReadPosRankSum=0.058;TLOD=6.18;ANN=A|downstream_gene_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000427897|protein_coding||c.*3354_*3356delCTC|||||3356|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000498495|processed_transcript||n.*4973_*4975delCTC|||||4975|,A|intron_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000374695|protein_coding|33/96|c.4221+2681_4221+2683delCTC|||||| GT:AD:AF:DP 0/1:22,3:0.1:25 0/0:12,0:0:12 | |
| chr1 22200999 . G T . t_lod_fstar ClippingRankSum=0;DP=40;ECNT=1;FS=2.944;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.91;ReadPosRankSum=-1.475;TLOD=4.23;ANN=T|synonymous_variant|LOW|HSPG2|ENSG00000142798|transcript|ENST00000374695|protein_coding|28/97|c.3556C>A|p.Arg1186Arg|3636/14327|3556/13176|1186/4391||,T|synonymous_variant|LOW|HSPG2|ENSG00000142798|transcript|ENST00000427897|protein_coding|2/5|c.118C>A|p.Arg40Arg|119/589|118/588|40/195||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000480900|retained_intron||n.*3008C>A|||||3008|,T|non_coding_transcript_exon_variant|MODIFIER|HSPG2|ENSG00000142798|transcript|ENST00000498495|processed_transcript|3/3|n.460C>A|||||| GT:AD:AF:DP 0/1:21,2:0.111:23 0/0:17,0:0:17 | |
| chr1 22332071 . T C . germline_risk;t_lod_fstar ClippingRankSum=0;DP=130;ECNT=1;FS=16.886;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=58.32;MQ0=0;MQRankSum=-8.712;NLOD=0.908;ReadPosRankSum=-3.923;TLOD=6.20;ANN=C|upstream_gene_variant|MODIFIER|RN7SL768P|ENSG00000263582|transcript|ENST00000584415|misc_RNA||n.-1710A>G|||||1710|,C|upstream_gene_variant|MODIFIER|CELA3A|ENSG00000142789|transcript|ENST00000400271|protein_coding||c.-1872T>C|||||1872|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|CELA3A|ENSG00000142789|transcript|ENST00000290122|protein_coding|3/7|c.227+34T>C||||||,C|intron_variant|MODIFIER|CELA3A|ENSG00000142789|transcript|ENST00000374663|protein_coding|3/3|c.227+34T>C|||||| GT:AD:AF:DP 0/1:80,5:0.077:85 0/0:38,3:0.097:41 | |
| chr1 22902691 . G T . t_lod_fstar ClippingRankSum=0;DP=61;ECNT=1;FS=3.072;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.01;ReadPosRankSum=1.38;TLOD=4.01;ANN=T|intron_variant|MODIFIER|EPHA8|ENSG00000070886|transcript|ENST00000166244|protein_coding|2/16|c.160-19G>T||||||,T|intron_variant|MODIFIER|EPHA8|ENSG00000070886|transcript|ENST00000374644|protein_coding|2/4|c.160-19G>T||||||,T|intron_variant|MODIFIER|EPHA8|ENSG00000070886|transcript|ENST00000538803|protein_coding|3/5|c.160-19G>T|||||| GT:AD:AF:DP 0/1:47,2:0.063:49 0/0:12,0:0:12 | |
| chr1 22929890 . A C . t_lod_fstar ClippingRankSum=0;DP=61;ECNT=1;FS=51.444;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.96;ReadPosRankSum=-0.029;TLOD=6.18;ANN=C|3_prime_UTR_variant|MODIFIER|EPHA8|ENSG00000070886|transcript|ENST00000166244|protein_coding|17/17|c.*1656A>C|||||1656| GT:AD:AF:DP 0/1:20,6:0.19:26 0/0:31,4:0.148:35 | |
| chr1 23346116 . CGCG C . germline_risk ClippingRankSum=0;DP=24;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.50;ReadPosRankSum=-0.609;TLOD=6.76;ANN=C|disruptive_inframe_deletion|MODERATE|KDM1A|ENSG00000004487|transcript|ENST00000400181|protein_coding|1/21|c.39_41delGGC|p.Ala14del|143/3059|39/2631|13/876||INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|KDM1A|ENSG00000004487|transcript|ENST00000356634|protein_coding|1/19|c.39_41delGGC|p.Ala14del|188/3033|39/2559|13/852||INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|KDM1A|ENSG00000004487|transcript|ENST00000542151|protein_coding|1/21|c.39_41delGGC|p.Ala14del|141/3058|39/2631|13/876||INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|C1orf234|ENSG00000227868|transcript|ENST00000566855|protein_coding||c.-3853_-3851delCGC|||||3774|,C|downstream_gene_variant|MODIFIER|RP1-184J9.2|ENSG00000240553|transcript|ENST00000427154|antisense||n.*521_*523delCGC|||||523| GT:AD:AF:DP 0/1:13,4:0.182:17 0/0:6,0:0:6 | |
| chr1 24080606 . GGAA G . t_lod_fstar ClippingRankSum=0;DP=246;ECNT=1;FS=6.193;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=16.84;ReadPosRankSum=-1.19;TLOD=4.73;ANN=G|disruptive_inframe_deletion|MODERATE|TCEB3|ENSG00000011007|transcript|ENST00000418390|protein_coding|6/11|c.1643_1645delAAG|p.Glu548del|1914/5154|1643/2397|548/798||INFO_REALIGN_3_PRIME,G|disruptive_inframe_deletion|MODERATE|TCEB3|ENSG00000011007|transcript|ENST00000609199|protein_coding|6/11|c.1565_1567delAAG|p.Glu522del|1597/2671|1565/2319|522/772||INFO_REALIGN_3_PRIME,G|downstream_gene_variant|MODIFIER|TCEB3|ENSG00000011007|transcript|ENST00000487554|processed_transcript||n.*3173_*3175delGAA|||||3173| GT:AD:AF:DP 0/1:143,2:0.02:145 0/0:85,0:0:85 | |
| chr1 25599204 . A C . PASS ClippingRankSum=0;DP=184;ECNT=1;FS=25.45;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=54.66;MQ0=13;MQRankSum=-6.496;NLOD=16.77;ReadPosRankSum=-2.954;TLOD=16.15;ANN=C|upstream_gene_variant|MODIFIER|C1orf63|ENSG00000117616|transcript|ENST00000568701|protein_coding||c.-25750T>G|||||4798|WARNING_TRANSCRIPT_NO_STOP_CODON,C|upstream_gene_variant|MODIFIER|C1orf63|ENSG00000117616|transcript|ENST00000450820|processed_transcript||n.-4828T>G|||||4828|,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000342055|protein_coding|1/8|c.148+18A>C||||||,C|intron_variant|MODIFIER|C1orf63|ENSG00000117616|transcript|ENST00000473314|nonsense_mediated_decay|1/5|c.-66-25684T>G||||||,C|intron_variant|MODIFIER|C1orf63|ENSG00000117616|transcript|ENST00000561867|protein_coding|1/1|c.-66-25684T>G||||||WARNING_TRANSCRIPT_NO_STOP_CODON,C|intron_variant|MODIFIER|C1orf63|ENSG00000117616|transcript|ENST00000568996|protein_coding|1/1|c.-66-25684T>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000564398|retained_intron|1/6|n.303+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000328664|protein_coding|1/9|c.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000454452|protein_coding|1/6|c.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000423253|processed_transcript|1/6|n.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000357542|protein_coding|1/7|c.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000417538|protein_coding|1/7|c.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000423810|protein_coding|1/9|c.148+18A>C||||||,C|intron_variant|MODIFIER|RHD|ENSG00000187010|transcript|ENST00000568195|protein_coding|1/8|c.148+18A>C|||||| GT:AD:AF:DP 0/1:70,9:0.122:79 0/0:85,2:0.029:87 | |
| chr1 26129127 . G A . germline_risk;t_lod_fstar ClippingRankSum=0;DP=18;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.10;ReadPosRankSum=-2.192;TLOD=4.49;ANN=A|intron_variant|MODIFIER|SEPN1|ENSG00000162430|transcript|ENST00000361547|protein_coding|3/12|c.403+519G>A||||||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,A|intron_variant|MODIFIER|SEPN1|ENSG00000162430|transcript|ENST00000354177|protein_coding|2/12|c.301+1476G>A||||||,A|intron_variant|MODIFIER|SEPN1|ENSG00000162430|transcript|ENST00000374315|protein_coding|2/11|c.301+1476G>A|||||| GT:AD:AF:DP 0/1:9,2:0.182:11 0/0:7,0:0:7 | |
| chr1 26517929 . G T . t_lod_fstar ClippingRankSum=0;DP=45;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.01;ReadPosRankSum=1.268;TLOD=4.39;ANN=T|splice_region_variant&intron_variant|LOW|CATSPER4|ENSG00000188782|transcript|ENST00000338855|protein_coding|2/8|c.357+8G>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,T|splice_region_variant&intron_variant|LOW|CATSPER4|ENSG00000188782|transcript|ENST00000456354|protein_coding|2/9|c.357+8G>T||||||,T|splice_region_variant&intron_variant|LOW|CATSPER4|ENSG00000188782|transcript|ENST00000518899|nonsense_mediated_decay|2/9|c.357+8G>T||||||,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000374253|protein_coding||c.*1890G>T|||||1554|,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000361530|protein_coding||c.*1890G>T|||||1552|,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000482227|nonsense_mediated_decay||c.*8082G>T|||||1556|,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000531191|protein_coding||c.*1890G>T|||||1592|,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000528281|nonsense_mediated_decay||c.*7213G>T|||||2981|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000480617|retained_intron||n.*3137G>T|||||3137|,T|downstream_gene_variant|MODIFIER|CNKSR1|ENSG00000142675|transcript|ENST00000484874|retained_intron||n.*2585G>T|||||2585| GT:AD:AF:DP 0/1:27,3:0.095:30 0/0:14,0:0:14 | |
| chr1 26527809 . A C . germline_risk ClippingRankSum=0;DP=21;ECNT=2;FS=1.719;HCNT=1;MAX_ED=1;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.602;ReadPosRankSum=-2.321;TLOD=32.24;ANN=C|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000338855|protein_coding|8/8|c.1200-36A>C||||||WARNING_TRANSCRIPT_NO_STOP_CODON,C|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000456354|protein_coding|8/9|c.1200-36A>C||||||,C|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000518899|nonsense_mediated_decay|8/9|c.*31-36A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:5,12:0.667:17:0|1:26527809_A_C 0/0:4,0:0:4:0|1:26527809_A_C | |
| chr1 26527810 . G A . germline_risk ClippingRankSum=0;DP=21;ECNT=2;FS=1.719;HCNT=1;MAX_ED=1;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.602;ReadPosRankSum=-2.321;TLOD=32.24;ANN=A|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000338855|protein_coding|8/8|c.1200-35G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000456354|protein_coding|8/9|c.1200-35G>A||||||,A|intron_variant|MODIFIER|CATSPER4|ENSG00000188782|transcript|ENST00000518899|nonsense_mediated_decay|8/9|c.*31-35G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:5,12:0.667:17:0|1:26527809_A_C 0/0:4,0:0:4:0|1:26527809_A_C | |
| chr1 26536563 . G T . t_lod_fstar ClippingRankSum=0;DP=194;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.40;ReadPosRankSum=0.336;TLOD=4.65;ANN=T|non_coding_transcript_exon_variant|MODIFIER|RP11-231P20.2|ENSG00000236155|transcript|ENST00000428812|transcribed_unprocessed_pseudogene|1/8|n.332G>T|||||| GT:AD:AF:DP 0/1:125,6:0.034:131 0/0:63,0:0:63 | |
| chr1 26773811 . CA C . PASS ClippingRankSum=0;DP=224;ECNT=1;FS=2.633;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.83;ReadPosRankSum=-0.032;TLOD=45.02;ANN=C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000374186|retained_intron||n.*4241delA|||||4241|,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000531312|protein_coding||c.*937delA|||||937|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000525165|protein_coding||c.*962delA|||||962|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000525326|protein_coding||c.*4558delA|||||4558|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000525546|protein_coding||c.*4516delA|||||4516|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000528557|processed_transcript||n.*4432delA|||||4432|,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000526278|retained_intron||n.*889delA|||||889|,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000529688|retained_intron||n.*939delA|||||939|,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000531955|processed_transcript||n.*4432delA|||||4432|,C|downstream_gene_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000525410|retained_intron||n.*925delA|||||925|,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000360009|protein_coding|5/8|c.441-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000434391|nonsense_mediated_decay|5/8|c.*242-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000427245|protein_coding|5/6|c.441-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000525682|protein_coding|5/7|c.440+898delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000236342|protein_coding|5/8|c.441-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000526219|protein_coding|4/7|c.324-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000374185|protein_coding|5/5|c.441-229delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000533087|protein_coding|5/5|c.441-229delA||||||WARNING_TRANSCRIPT_INCOMPLETE&INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000436153|protein_coding|5/5|c.441-229delA||||||WARNING_TRANSCRIPT_INCOMPLETE&INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000430232|protein_coding|3/5|c.324-229delA||||||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000431933|protein_coding|2/3|c.155+898delA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|DHDDS|ENSG00000117682|transcript|ENST00000416052|protein_coding|1/4|c.69-229delA||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:64,72:0.552:136 0/0:69,5:0.089:74 | |
| chr1 27100181 . CGCA C . t_lod_fstar ClippingRankSum=0;DP=86;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.70;ReadPosRankSum=-1.355;TLOD=4.77;ANN=C|disruptive_inframe_deletion|MODERATE|ARID1A|ENSG00000117713|transcript|ENST00000324856|protein_coding|16/20|c.3999_4001delGCA|p.Gln1334del|4370/8577|3999/6858|1333/2285||INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|ARID1A|ENSG00000117713|transcript|ENST00000457599|protein_coding|16/20|c.3999_4001delGCA|p.Gln1334del|3999/6268|3999/6207|1333/2068||INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|ARID1A|ENSG00000117713|transcript|ENST00000374152|protein_coding|15/19|c.2850_2852delGCA|p.Gln951del|3133/5992|2850/5709|950/1902||INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|ARID1A|ENSG00000117713|transcript|ENST00000430799|protein_coding|5/9|c.687_689delGCA|p.Gln230del|688/3978|687/3546|229/1181||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,C|disruptive_inframe_deletion|MODERATE|ARID1A|ENSG00000117713|transcript|ENST00000466382|nonsense_mediated_decay|3/6|c.306_308delGCA|p.Gln103del|308/2696|306/432|102/143||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,C|sequence_feature|MODERATE|ARID1A|ENSG00000117713|compositionally-biased-region:Gln-rich|ENST00000324856|protein_coding|16/20|c.3978_3980delGCA||||||,C|5_prime_UTR_variant|MODIFIER|ARID1A|ENSG00000117713|transcript|ENST00000540690|protein_coding|3/6|c.-126_-124delGCA|||||1886|INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|ARID1A|ENSG00000117713|transcript|ENST00000532781|nonsense_mediated_decay||c.-1181_-1179delGCA|||||1179|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:52,3:0.048:55 0/0:24,0:0:24 | |
| chr1 27875352 . AAGG A . t_lod_fstar ClippingRankSum=0;DP=66;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.21;ReadPosRankSum=0.623;TLOD=6.19;ANN=A|disruptive_inframe_deletion|MODERATE|AHDC1|ENSG00000126705|transcript|ENST00000247087|protein_coding|5/6|c.3272_3274delCCT|p.Ser1091del|3871/6334|3272/4812|1091/1603||,A|disruptive_inframe_deletion|MODERATE|AHDC1|ENSG00000126705|transcript|ENST00000374011|protein_coding|6/7|c.3272_3274delCCT|p.Ser1091del|4243/6438|3272/4812|1091/1603||,A|downstream_gene_variant|MODIFIER|AHDC1|ENSG00000126705|transcript|ENST00000487743|processed_transcript||n.*3198_*3200delCCT|||||3200|,A|downstream_gene_variant|MODIFIER|AHDC1|ENSG00000126705|transcript|ENST00000490295|processed_transcript||n.*3883_*3885delCCT|||||3885| GT:AD:AF:DP 0/1:25,3:0.118:28 0/0:18,0:0:18 | |
| chr1 28476678 . G T . t_lod_fstar ClippingRankSum=0;DP=139;ECNT=1;FS=4.74;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.23;ReadPosRankSum=0.15;TLOD=4.71;ANN=T|missense_variant|MODERATE|PTAFR|ENSG00000169403|transcript|ENST00000305392|protein_coding|2/2|c.855C>A|p.Asn285Lys|1045/1539|855/1029|285/342||,T|missense_variant|MODERATE|PTAFR|ENSG00000169403|transcript|ENST00000373857|protein_coding|2/2|c.855C>A|p.Asn285Lys|1490/4491|855/1029|285/342||,T|missense_variant|MODERATE|PTAFR|ENSG00000169403|transcript|ENST00000539896|protein_coding|3/3|c.855C>A|p.Asn285Lys|1190/4191|855/1029|285/342|| GT:AD:AF:DP 0/1:90,5:0.041:95 0/0:44,0:0:44 | |
| chr1 31212838 . G A . t_lod_fstar ClippingRankSum=0;DP=43;ECNT=1;FS=5.714;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.40;ReadPosRankSum=0.687;TLOD=6.28;ANN=A|upstream_gene_variant|MODIFIER|MIR4420|ENSG00000264773|transcript|ENST00000583944|miRNA||n.-759C>T|||||759|,A|downstream_gene_variant|MODIFIER|LAPTM5|ENSG00000162511|transcript|ENST00000476492|processed_transcript||n.*1698C>T|||||1698|,A|intron_variant|MODIFIER|LAPTM5|ENSG00000162511|transcript|ENST00000294507|protein_coding|3/7|c.259-54C>T||||||,A|intron_variant|MODIFIER|LAPTM5|ENSG00000162511|transcript|ENST00000464569|processed_transcript|3/7|n.484-54C>T|||||| GT:AD:AF:DP 0/1:28,3:0.13:31 0/0:10,0:0:10 | |
| chr1 32950824 . CGAT C . t_lod_fstar ClippingRankSum=0;DP=117;ECNT=1;FS=0;HCNT=43;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=-1.706;TLOD=5.16;ANN=C|conservative_inframe_deletion|MODERATE|RP1-27O5.3|ENSG00000254553|transcript|ENST00000480336|nonsense_mediated_decay|4/10|c.1306_1308delGAT|p.Asp436del|1396/3447|1306/1539|436/512||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|ZBTB8B|ENSG00000273274|transcript|ENST00000609129|protein_coding|4/4|c.1306_1308delGAT|p.Asp436del|1384/12834|1306/1488|436/495||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:81,3:0.032:84 0/0:26,0:0:26 | |
| chr1 33476350 . C T . PASS ClippingRankSum=0;DP=180;ECNT=1;FS=3.187;HCNT=27;MAX_ED=.;MIN_ED=.;MQ=59.38;MQ0=0;MQRankSum=-8.239;NLOD=6.06;ReadPosRankSum=-1.627;TLOD=6.63;ANN=T|3_prime_UTR_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000373449|protein_coding|7/7|c.*80G>A|||||80|,T|3_prime_UTR_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000548033|protein_coding|6/6|c.*80G>A|||||80|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000354858|protein_coding||c.*2432G>A|||||2295|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000467905|protein_coding||c.*1369G>A|||||6|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000480134|protein_coding||c.*3774G>A|||||2295|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000550338|nonsense_mediated_decay||c.*20877G>A|||||2458|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000469238|retained_intron||n.*3616G>A|||||3616|,T|downstream_gene_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000466029|retained_intron||n.*3734G>A|||||3734|,T|intron_variant|MODIFIER|RP1-117O3.2|ENSG00000236065|transcript|ENST00000427524|antisense|1/1|n.246-20286C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000482191|retained_intron|2/2|n.369G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|AK2|ENSG00000004455|transcript|ENST00000491241|processed_transcript|4/4|n.478G>A|||||| GT:AD:AF:DP 0/1:127,6:0.043:133 0/0:44,2:0.031:46 | |
| chr1 34497602 . TTAA T . t_lod_fstar ClippingRankSum=0;DP=255;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.41;ReadPosRankSum=0.102;TLOD=4.73;ANN=T|intron_variant|MODIFIER|CSMD2|ENSG00000121904|transcript|ENST00000373381|protein_coding|3/70|c.517+590_517+592delTTA||||||,T|intron_variant|MODIFIER|CSMD2|ENSG00000121904|transcript|ENST00000241312|nonsense_mediated_decay|3/69|c.397+590_397+592delTTA|||||| GT:AD:AF:DP 0/1:140,3:0.02:143 0/0:64,0:0:64 | |
| chr1 35879693 . AT A . t_lod_fstar ClippingRankSum=0;DP=385;ECNT=1;FS=1.592;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.24;ReadPosRankSum=-1.273;TLOD=4.31;ANN=A|intron_variant|MODIFIER|ZMYM4|ENSG00000146463|transcript|ENST00000314607|protein_coding|27/29|c.4060+19delT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|ZMYM4|ENSG00000146463|transcript|ENST00000373297|protein_coding|25/27|c.3793+19delT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|ZMYM4|ENSG00000146463|transcript|ENST00000457946|protein_coding|21/23|c.3034+19delT||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:232,29:0.12:261 0/0:82,3:0.052:85 | |
| chr1 37948212 . C G . germline_risk ClippingRankSum=0;DP=73;ECNT=1;FS=0;HCNT=80;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.39;ReadPosRankSum=-0.225;TLOD=100.71;ANN=G|downstream_gene_variant|MODIFIER|ZC3H12A|ENSG00000163874|transcript|ENST00000472312|retained_intron||n.*849C>G|||||849|,G|downstream_gene_variant|MODIFIER|ZC3H12A|ENSG00000163874|transcript|ENST00000471012|protein_coding||c.*9C>G|||||9|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZC3H12A|ENSG00000163874|transcript|ENST00000373087|protein_coding|5/5|c.925+71C>G|||||| GT:AD:AF:DP 0/1:8,46:0.85:54 0/0:18,1:0.071:19 | |
| chr1 39550031 . G T . t_lod_fstar ClippingRankSum=0;DP=61;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.31;ReadPosRankSum=-0.556;TLOD=4.01;ANN=T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000567887|protein_coding|1/101|c.141G>T|p.Leu47Leu|298/24319|141/22779|47/7592||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000484793|protein_coding|3/4|c.141G>T|p.Leu47Leu|476/834|141/366|47/121||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000602421|protein_coding|2/3|c.141G>T|p.Leu47Leu|320/1423|141/366|47/121||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000545844|protein_coding|2/94|c.141G>T|p.Leu47Leu|249/17724|141/16293|47/5430||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000372915|protein_coding|1/97|c.141G>T|p.Leu47Leu|228/23440|141/22167|47/7388||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000361689|protein_coding|1/93|c.141G>T|p.Leu47Leu|193/17538|141/16293|47/5430||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000317713|protein_coding|1/93|c.141G>T|p.Leu47Leu|193/17668|141/16293|47/5430||,T|synonymous_variant|LOW|MACF1|ENSG00000127603|transcript|ENST00000539005|protein_coding|1/91|c.141G>T|p.Leu47Leu|193/17278|141/15903|47/5300|| GT:AD:AF:DP 0/1:41,3:0.063:44 0/0:17,0:0:17 | |
| chr1 40428785 . C G . PASS ClippingRankSum=0;DP=92;ECNT=1;FS=0;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=59.93;MQ0=0;MQRankSum=-1.029;NLOD=8.12;ReadPosRankSum=-1.657;TLOD=65.00;ANN=G|upstream_gene_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000480630|processed_transcript||n.-1098C>G|||||1098|,G|upstream_gene_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000491515|processed_transcript||n.-3549C>G|||||3549|,G|upstream_gene_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000459917|processed_transcript||n.-4370C>G|||||4370|,G|upstream_gene_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000481612|processed_transcript||n.-4506C>G|||||4506|,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000372809|protein_coding|3/13|c.393-2098C>G||||||,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000372811|protein_coding|3/13|c.354-2098C>G||||||,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000420632|protein_coding|1/11|c.-115-2098C>G||||||,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000434861|protein_coding|3/6|c.348-2098C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000483824|processed_transcript|3/11|n.489-2098C>G||||||,G|intron_variant|MODIFIER|MFSD2A|ENSG00000168389|transcript|ENST00000469745|processed_transcript|2/7|n.266-2098C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP3-342P20.2|ENSG00000228477|transcript|ENST00000438210|processed_pseudogene|1/1|n.434C>G|||||| GT:AD:AF:DP 0/1:21,35:0.622:56 0/0:35,0:0:35 | |
| chr1 40704843 . G T . t_lod_fstar ClippingRankSum=0;DP=119;ECNT=1;FS=0;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.43;ReadPosRankSum=0.814;TLOD=4.47;ANN=T|missense_variant|MODERATE|RLF|ENSG00000117000|transcript|ENST00000372771|protein_coding|8/8|c.4469G>T|p.Ser1490Ile|4496/6246|4469/5745|1490/1914|| GT:AD:AF:DP 0/1:67,3:0.054:70 0/0:49,0:0:49 | |
| chr1 43317166 . G T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=29;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.11;ReadPosRankSum=0.434;TLOD=4.24;ANN=T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000397044|protein_coding|3/3|c.630G>T|p.Gln210His|1020/1452|630/948|210/315||,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372508|protein_coding|2/2|c.537G>T|p.Gln179His|595/1577|537/855|179/284||,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372507|protein_coding|3/3|c.537G>T|p.Gln179His|701/1683|537/855|179/284||,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372506|protein_coding|4/4|c.537G>T|p.Gln179His|877/1859|537/855|179/284||,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372504|protein_coding|5/5|c.603G>T|p.Gln201His|953/1935|603/921|201/306||,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372503|protein_coding|2/2|c.630G>T|p.Gln210His|734/993|630/889|210/295||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|ZNF691|ENSG00000164011|transcript|ENST00000372502|protein_coding|2/2|c.603G>T|p.Gln201His|603/1581|603/921|201/306||,T|downstream_gene_variant|MODIFIER|ZNF691|ENSG00000164011|transcript|ENST00000397034|protein_coding||c.*231G>T|||||231|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:20,2:0.125:22 0/0:7,0:0:7 | |
| chr1 43353838 . G A . t_lod_fstar ClippingRankSum=0;DP=56;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.91;ReadPosRankSum=0.534;TLOD=4.63;ANN=A|downstream_gene_variant|MODIFIER|RP11-342M1.6|ENSG00000237090|transcript|ENST00000417517|processed_pseudogene||n.*2927C>T|||||2927|,A|non_coding_transcript_exon_variant|MODIFIER|RP11-342M1.7|ENSG00000233708|transcript|ENST00000448759|processed_pseudogene|2/5|n.479C>T|||||| GT:AD:AF:DP 0/1:40,1:0.063:41 0/0:15,0:0:15 | |
| chr1 45098099 . TCCTC T . t_lod_fstar ClippingRankSum=0;DP=53;ECNT=1;FS=0;HCNT=36;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.00;ReadPosRankSum=0.333;TLOD=6.17;ANN=T|upstream_gene_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000484745|processed_transcript||n.-217_-214delCCTC|||||217|,T|downstream_gene_variant|MODIFIER|TMEM53|ENSG00000126106|transcript|ENST00000372242|protein_coding||c.*3979_*3982delGAGG|||||2810|,T|downstream_gene_variant|MODIFIER|TMEM53|ENSG00000126106|transcript|ENST00000372243|protein_coding||c.*3979_*3982delGAGG|||||2810|,T|downstream_gene_variant|MODIFIER|TMEM53|ENSG00000126106|transcript|ENST00000372244|protein_coding||c.*3956_*3959delGAGG|||||2810|,T|downstream_gene_variant|MODIFIER|TMEM53|ENSG00000126106|transcript|ENST00000495630|processed_transcript||n.*3617_*3620delGAGG|||||3620|,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000355387|protein_coding|6/14|c.949+55_949+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000361799|protein_coding|6/14|c.949+55_949+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000372247|protein_coding|5/13|c.949+55_949+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000443020|protein_coding|5/13|c.232+55_232+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000453863|protein_coding|2/3|c.115+55_115+58delCCTC||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000335497|protein_coding|2/8|c.97+55_97+58delCCTC||||||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000440132|protein_coding|2/9|c.97+55_97+58delCCTC||||||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000474064|processed_transcript|2/9|n.288+55_288+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000471494|processed_transcript|2/5|n.281+55_281+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000488865|nonsense_mediated_decay|2/3|c.101+55_101+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000497469|processed_transcript|1/4|n.151+55_151+58delCCTC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RNF220|ENSG00000187147|transcript|ENST00000475378|processed_transcript|1/9|n.131+55_131+58delCCTC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:18,2:0.111:20 0/0:10,0:0:10 | |
| chr1 46184896 . AAC A . t_lod_fstar ClippingRankSum=0;DP=81;ECNT=1;FS=0;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.02;ReadPosRankSum=-0.084;TLOD=4.07;ANN=A|frameshift_variant|HIGH|IPP|ENSG00000197429|transcript|ENST00000396478|protein_coding|6/9|c.1163_1164delGT|p.Cys388fs|1267/3113|1163/1755|388/584||,A|frameshift_variant|HIGH|IPP|ENSG00000197429|transcript|ENST00000359942|protein_coding|6/10|c.1163_1164delGT|p.Cys388fs|1268/1947|1163/1749|388/582||,A|upstream_gene_variant|MODIFIER|IPP|ENSG00000197429|transcript|ENST00000495072|processed_transcript||n.-4974_-4973delGT|||||4973|;LOF=(IPP|ENSG00000197429|4|0.50) GT:AD:AF:DP 0/1:48,2:0.051:50 0/0:27,0:0:27 | |
| chr1 47182032 . C T . t_lod_fstar ClippingRankSum=0;DP=272;ECNT=1;FS=15.123;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=59.68;MQ0=2;MQRankSum=0;NLOD=17.15;ReadPosRankSum=-0.063;TLOD=5.33;ANN=T|missense_variant|MODERATE|EFCAB14|ENSG00000159658|transcript|ENST00000371933|protein_coding|2/11|c.269G>A|p.Gly90Asp|1246/5767|269/1488|90/495||,T|missense_variant|MODERATE|EFCAB14|ENSG00000159658|transcript|ENST00000544071|protein_coding|2/11|c.269G>A|p.Gly90Asp|1334/2338|269/1257|90/418|| GT:AD:AF:DP 0/1:186,4:0.027:190 0/0:73,0:0:73 | |
| chr1 51820407 . G T . t_lod_fstar ClippingRankSum=0;DP=358;ECNT=1;FS=0;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=32.50;ReadPosRankSum=0.955;TLOD=4.08;ANN=T|3_prime_UTR_variant|MODIFIER|EPS15|ENSG00000085832|transcript|ENST00000371733|protein_coding|25/25|c.*1965C>A|||||1965|,T|3_prime_UTR_variant|MODIFIER|EPS15|ENSG00000085832|transcript|ENST00000371730|protein_coding|23/23|c.*1965C>A|||||1965|,T|downstream_gene_variant|MODIFIER|EPS15|ENSG00000085832|transcript|ENST00000396122|protein_coding||c.*1965C>A|||||1574| GT:AD:AF:DP 0/1:212,4:0.019:216 0/0:141,0:0:141 | |
| chr1 52256200 . G T . t_lod_fstar ClippingRankSum=0;DP=120;ECNT=1;FS=1.959;HCNT=76;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.73;ReadPosRankSum=1.77;TLOD=4.48;ANN=T|splice_region_variant&intron_variant|LOW|NRD1|ENSG00000078618|transcript|ENST00000354831|protein_coding|31/32|c.3372+5C>A||||||,T|splice_region_variant&intron_variant|LOW|NRD1|ENSG00000078618|transcript|ENST00000440943|protein_coding|14/15|c.1326+5C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|splice_region_variant&intron_variant|LOW|NRD1|ENSG00000078618|transcript|ENST00000352171|protein_coding|29/30|c.3168+5C>A||||||,T|splice_region_variant&intron_variant|LOW|NRD1|ENSG00000078618|transcript|ENST00000485608|processed_transcript|29/30|n.2837+5C>A||||||,T|splice_region_variant&intron_variant|LOW|NRD1|ENSG00000078618|transcript|ENST00000539524|protein_coding|31/32|c.2976+5C>A||||||,T|upstream_gene_variant|MODIFIER|RP4-657D16.3|ENSG00000266993|transcript|ENST00000586761|antisense||n.-3457G>T|||||3457|,T|upstream_gene_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000464385|processed_transcript||n.-706C>A|||||706|,T|upstream_gene_variant|MODIFIER|RP4-657D16.3|ENSG00000266993|transcript|ENST00000588291|antisense||n.-3437G>T|||||3437|,T|upstream_gene_variant|MODIFIER|RP4-657D16.3|ENSG00000266993|transcript|ENST00000591675|antisense||n.-4683G>T|||||4683|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000371710|protein_coding||c.*2739G>T|||||1311|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000371714|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000337809|protein_coding||c.*2739G>T|||||1311|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000435274|nonsense_mediated_decay||c.*120906G>T|||||2562|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000435686|protein_coding||c.*2739G>T|||||2064|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000447887|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000495776|nonsense_mediated_decay||c.*76484G>T|||||2059|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000428468|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000453295|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000530544|protein_coding||c.*2739G>T|||||2562|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000531828|protein_coding||c.*2739G>T|||||2739|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000361556|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000462759|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000486942|protein_coding||c.*2739G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000475697|retained_intron||n.*2059G>T|||||2059|,T|downstream_gene_variant|MODIFIER|OSBPL9|ENSG00000117859|transcript|ENST00000531819|retained_intron||n.*2064G>T|||||2064|,T|downstream_gene_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000475310|processed_transcript||n.*3944C>A|||||3944|,T|downstream_gene_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000497358|processed_transcript||n.*3944C>A|||||3944|,T|downstream_gene_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000544028|protein_coding||c.*4645C>A|||||4059| GT:AD:AF:DP 0/1:70,4:0.042:74 0/0:46,0:0:46 | |
| chr1 52306063 . ATCT A . t_lod_fstar ClippingRankSum=0;DP=203;ECNT=1;FS=0;HCNT=30;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=-0.517;TLOD=4.93;ANN=A|disruptive_inframe_deletion|MODERATE|NRD1|ENSG00000078618|transcript|ENST00000354831|protein_coding|2/33|c.462_464delAGA|p.Glu154del|654/3895|462/3660|154/1219||,A|disruptive_inframe_deletion|MODERATE|NRD1|ENSG00000078618|transcript|ENST00000352171|protein_coding|2/31|c.462_464delAGA|p.Glu154del|654/3691|462/3456|154/1151||,A|disruptive_inframe_deletion|MODERATE|NRD1|ENSG00000078618|transcript|ENST00000539524|protein_coding|2/33|c.66_68delAGA|p.Glu22del|160/3380|66/3264|22/1087||,A|disruptive_inframe_deletion|MODERATE|NRD1|ENSG00000078618|transcript|ENST00000544028|protein_coding|2/25|c.66_68delAGA|p.Glu22del|210/2557|66/2244|22/747||,A|upstream_gene_variant|MODIFIER|MIR761|ENSG00000212076|transcript|ENST00000390787|miRNA||n.-3984_-3982delAGA|||||3982|,A|upstream_gene_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000475715|processed_transcript||n.-2822_-2820delAGA|||||2820|,A|non_coding_transcript_exon_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000485608|processed_transcript|1/31|n.61_63delAGA||||||,A|non_coding_transcript_exon_variant|MODIFIER|NRD1|ENSG00000078618|transcript|ENST00000491410|processed_transcript|2/2|n.618_620delAGA|||||| GT:AD:AF:DP 0/1:111,3:0.025:114 0/0:54,1:0.026:55 | |
| chr1 53986334 . A C . t_lod_fstar ClippingRankSum=0;DP=94;ECNT=1;FS=20.912;HCNT=60;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.18;ReadPosRankSum=-2.004;TLOD=4.08;ANN=C|missense_variant|MODERATE|GLIS1|ENSG00000174332|transcript|ENST00000312233|protein_coding|6/10|c.1174T>G|p.Cys392Gly|1741/2812|1174/1863|392/620|| GT:AD:AF:DP 0/1:56,4:0.089:60 0/0:30,1:0.042:31 | |
| chr1 54298189 . CTTA C . PASS ClippingRankSum=0;DP=316;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.30;ReadPosRankSum=0.29;TLOD=7.36;ANN=C|disruptive_inframe_deletion|MODERATE|NDC1|ENSG00000058804|transcript|ENST00000371429|protein_coding|3/18|c.251_253delTAA|p.Ile84del|852/5134|251/2025|84/674||,C|disruptive_inframe_deletion|MODERATE|NDC1|ENSG00000058804|transcript|ENST00000540001|protein_coding|3/17|c.251_253delTAA|p.Ile84del|544/4713|251/1629|84/542||,C|5_prime_UTR_variant|MODIFIER|NDC1|ENSG00000058804|transcript|ENST00000537333|protein_coding|2/16|c.-619_-617delTAA|||||28529|,C|5_prime_UTR_variant|MODIFIER|NDC1|ENSG00000058804|transcript|ENST00000234725|protein_coding|2/17|c.-95_-93delTAA|||||4409|,C|downstream_gene_variant|MODIFIER|AL049745.1|ENSG00000264454|transcript|ENST00000578163|miRNA||n.*3656_*3658delTTA|||||3656|,C|non_coding_transcript_exon_variant|MODIFIER|NDC1|ENSG00000058804|transcript|ENST00000480952|processed_transcript|2/5|n.332_334delTAA|||||| GT:AD:AF:DP 0/1:197,6:0.024:203 0/0:76,2:0.039:78 | |
| chr1 55078271 . TCTC T . t_lod_fstar ClippingRankSum=0;DP=105;ECNT=1;FS=1.725;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60.1;MQ0=0;MQRankSum=4.472;NLOD=5.11;ReadPosRankSum=0.543;TLOD=5.47;ANN=T|conservative_inframe_deletion|MODERATE|FAM151A|ENSG00000162391|transcript|ENST00000302250|protein_coding|5/8|c.685_687delGAG|p.Glu229del|848/2005|685/1758|229/585||,T|conservative_inframe_deletion|MODERATE|FAM151A|ENSG00000162391|transcript|ENST00000371304|protein_coding|5/7|c.685_687delGAG|p.Glu229del|848/1444|685/1197|229/398||,T|downstream_gene_variant|MODIFIER|ACOT11|ENSG00000162390|transcript|ENST00000481208|processed_transcript||n.*2475_*2477delCTC|||||2475|,T|downstream_gene_variant|MODIFIER|ACOT11|ENSG00000162390|transcript|ENST00000343744|protein_coding||c.*3487_*3489delCTC|||||2272|,T|intron_variant|MODIFIER|ACOT11|ENSG00000162390|transcript|ENST00000371316|protein_coding|15/16|c.1629+4532_1629+4534delTCC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:73,5:0.06:78 0/0:25,0:0:25 | |
| chr1 55470811 . G A . germline_risk;t_lod_fstar ClippingRankSum=0;DP=21;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.20;ReadPosRankSum=-0.203;TLOD=4.81;ANN=A|intron_variant|MODIFIER|BSND|ENSG00000162399|transcript|ENST00000371265|protein_coding|2/3|c.272+22G>A|||||| GT:AD:AF:DP 0/1:13,3:0.167:16 0/0:5,0:0:5 | |
| chr1 55505552 . ACTG A . t_lod_fstar ClippingRankSum=0;DP=168;ECNT=1;FS=2.358;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60.13;MQ0=0;MQRankSum=0;NLOD=10.62;ReadPosRankSum=0.729;TLOD=4.35;ANN=A|disruptive_inframe_deletion|MODERATE|PCSK9|ENSG00000169174|transcript|ENST00000302118|protein_coding|1/12|c.63_65delGCT|p.Leu22del|353/3637|63/2079|21/692||INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|PCSK9|ENSG00000169174|transcript|ENST00000452118|protein_coding|1/6|c.63_65delGCT|p.Leu22del|143/1101|63/618|21/205||INFO_REALIGN_3_PRIME,A|upstream_gene_variant|MODIFIER|PCSK9|ENSG00000169174|transcript|ENST00000543384|protein_coding||c.-12475_-12473delCTG|||||342| GT:AD:AF:DP 0/1:99,3:0.034:102 0/0:49,0:0:49 | |
| chr1 57085047 . C T . PASS ClippingRankSum=0;DP=246;ECNT=1;FS=19.437;HCNT=23;MAX_ED=.;MIN_ED=.;MQ=57.5;MQ0=2;MQRankSum=-4.147;NLOD=4.68;ReadPosRankSum=-1.019;TLOD=44.78;ANN=T|downstream_gene_variant|MODIFIER|RP11-377K22.2|ENSG00000225475|transcript|ENST00000442812|processed_pseudogene||n.*35G>A|||||35|,T|intron_variant|MODIFIER|PPAP2B|ENSG00000162407|transcript|ENST00000461655|processed_transcript|2/3|n.241+24094G>A||||||,T|intron_variant|MODIFIER|PPAP2B|ENSG00000162407|transcript|ENST00000476206|processed_transcript|2/2|n.180+24126G>A|||||| GT:AD:AF:DP 0/1:160,22:0.134:182 0/0:27,2:0.071:29 | |
| chr1 57409512 . GA G . t_lod_fstar ClippingRankSum=0;DP=185;ECNT=1;FS=4.221;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.42;ReadPosRankSum=-0.103;TLOD=4.58;ANN=G|intron_variant|MODIFIER|C8B|ENSG00000021852|transcript|ENST00000371237|protein_coding|7/11|c.1106-16delT||||||,G|intron_variant|MODIFIER|C8B|ENSG00000021852|transcript|ENST00000543257|protein_coding|8/12|c.950-16delT||||||,G|intron_variant|MODIFIER|C8B|ENSG00000021852|transcript|ENST00000535057|protein_coding|8/12|c.920-16delT|||||| GT:AD:AF:DP 0/1:118,5:0.049:123 0/0:53,0:0:53 | |
| chr1 62256200 . G T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=13;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=56.32;MQ0=0;MQRankSum=-0.908;NLOD=0.581;ReadPosRankSum=1.248;TLOD=6.29;ANN=T|intron_variant|MODIFIER|INADL|ENSG00000132849|transcript|ENST00000371158|protein_coding|8/42|c.1069-820G>T||||||,T|intron_variant|MODIFIER|INADL|ENSG00000132849|transcript|ENST00000316485|protein_coding|8/35|c.1069-820G>T||||||,T|intron_variant|MODIFIER|INADL|ENSG00000132849|transcript|ENST00000459752|retained_intron|8/33|n.1183-820G>T||||||,T|intron_variant|MODIFIER|INADL|ENSG00000132849|transcript|ENST00000484562|retained_intron|8/34|n.1183-820G>T|||||| GT:AD:AF:DP 0/1:5,4:0.5:9 0/0:2,0:0:2 | |
| chr1 62971443 . C T . t_lod_fstar ClippingRankSum=0;DP=225;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.66;ReadPosRankSum=-1.071;TLOD=4.62;ANN=T|synonymous_variant|LOW|DOCK7|ENSG00000116641|transcript|ENST00000251157|protein_coding|36/49|c.4494G>A|p.Val1498Val|4528/7110|4494/6390|1498/2129||,T|synonymous_variant|LOW|DOCK7|ENSG00000116641|transcript|ENST00000454575|protein_coding|16/30|c.2007G>A|p.Val669Val|2008/4426|2007/3909|669/1302||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|DOCK7|ENSG00000116641|transcript|ENST00000340370|protein_coding|35/49|c.4428G>A|p.Val1476Val|4446/6864|4428/6330|1476/2109|| GT:AD:AF:DP 0/1:135,5:0.031:140 0/0:84,0:0:84 | |
| chr1 65255182 . C T . PASS ClippingRankSum=0;DP=312;ECNT=1;FS=1.531;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.93;ReadPosRankSum=0.31;TLOD=8.77;ANN=T|stop_gained|HIGH|RAVER2|ENSG00000162437|transcript|ENST00000294428|protein_coding|5/12|c.1090C>T|p.Arg364*|1168/4398|1090/2076|364/691||,T|stop_gained|HIGH|RAVER2|ENSG00000162437|transcript|ENST00000371072|protein_coding|5/12|c.1090C>T|p.Arg364*|1168/4362|1090/2037|364/678||,T|stop_gained|HIGH|RAVER2|ENSG00000162437|transcript|ENST00000430964|protein_coding|3/7|c.208C>T|p.Arg70*|333/893|208/693|70/230||,T|stop_gained|HIGH|RAVER2|ENSG00000162437|transcript|ENST00000418058|nonsense_mediated_decay|3/8|c.208C>T|p.Arg70*|331/2531|208/501|70/166||;LOF=(RAVER2|ENSG00000162437|4|1.00);NMD=(RAVER2|ENSG00000162437|4|1.00) GT:AD:AF:DP 0/1:217,7:0.041:224 0/0:87,0:0:87 | |
| chr1 65693159 . A G . t_lod_fstar ClippingRankSum=0;DP=469;ECNT=1;FS=8.189;HCNT=41;MAX_ED=.;MIN_ED=.;MQ=45.01;MQ0=133;MQRankSum=-2.666;NLOD=14.70;ReadPosRankSum=-2.358;TLOD=4.89;ANN=G|3_prime_UTR_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000327299|protein_coding|5/5|c.*1299A>G|||||1299|,G|3_prime_UTR_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000545314|protein_coding|6/6|c.*1299A>G|||||1299|,G|3_prime_UTR_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000395334|protein_coding|6/6|c.*1299A>G|||||1299|,G|downstream_gene_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000497030|processed_transcript||n.*1384A>G|||||1384|,G|downstream_gene_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000470888|processed_transcript||n.*2639A>G|||||2639|,G|downstream_gene_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000546702|protein_coding||c.*1299A>G|||||585|,G|downstream_gene_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000474968|processed_transcript||n.*1037A>G|||||1037|,G|downstream_gene_variant|MODIFIER|AK4|ENSG00000162433|transcript|ENST00000479060|processed_transcript||n.*1047A>G|||||1047| GT:AD:AF:DP 0/1:186,4:0.029:190 0/0:131,0:0:131 | |
| chr1 67109410 . TTG T . t_lod_fstar ClippingRankSum=0;DP=89;ECNT=1;FS=5.28;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.30;ReadPosRankSum=0.304;TLOD=4.27;ANN=T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000237247|protein_coding|8/26|c.471+22_471+23delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000371039|protein_coding|7/21|c.387+22_387+23delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000424320|protein_coding|8/12|c.459+22_459+23delGT||||||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000371035|protein_coding|5/21|c.330+22_330+23delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000468286|processed_transcript|6/9|n.590+22_590+23delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000371036|protein_coding|6/20|c.384+22_384+23delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000371037|protein_coding|7/24|c.459+22_459+23delGT||||||INFO_REALIGN_3_PRIME,T|non_coding_transcript_exon_variant|MODIFIER|SGIP1|ENSG00000118473|transcript|ENST00000483060|processed_transcript|6/6|n.470_471delGT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:47,3:0.077:50 0/0:30,0:0:30 | |
| chr1 70705168 . TAGG T . t_lod_fstar ClippingRankSum=0;DP=190;ECNT=1;FS=6.145;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.62;ReadPosRankSum=0.651;TLOD=4.92;ANN=T|disruptive_inframe_deletion|MODERATE|SRSF11|ENSG00000116754|transcript|ENST00000370950|protein_coding|8/13|c.776_778delGGA|p.Arg259del|858/3784|776/1455|259/484||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SRSF11|ENSG00000116754|transcript|ENST00000370951|protein_coding|8/13|c.776_778delGGA|p.Arg259del|897/2385|776/1452|259/483||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SRSF11|ENSG00000116754|transcript|ENST00000405432|protein_coding|8/13|c.776_778delGGA|p.Arg259del|855/1534|776/1455|259/484||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SRSF11|ENSG00000116754|transcript|ENST00000395136|protein_coding|7/11|c.776_778delGGA|p.Arg259del|1017/1408|776/1167|259/388||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|SRSF11|ENSG00000116754|transcript|ENST00000370949|protein_coding|5/10|c.596_598delGGA|p.Arg199del|1159/3034|596/1275|199/424||INFO_REALIGN_3_PRIME,T|downstream_gene_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000475204|nonsense_mediated_decay||c.*7578_*7580delAGG|||||3936|,T|downstream_gene_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000436161|protein_coding||c.*7578_*7580delAGG|||||1930|,T|downstream_gene_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000486667|processed_transcript||n.*1936_*1938delAGG|||||1936|,T|downstream_gene_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000481648|processed_transcript||n.*4755_*4757delAGG|||||4755|,T|non_coding_transcript_exon_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000484162|processed_transcript|6/11|n.2137_2139delGGA||||||INFO_REALIGN_3_PRIME,T|non_coding_transcript_exon_variant|MODIFIER|SRSF11|ENSG00000116754|transcript|ENST00000463859|processed_transcript|2/8|n.130_132delGGA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:124,2:0.024:126 0/0:50,0:0:50 | |
| chr1 70877105 . GA G . t_lod_fstar ClippingRankSum=0;DP=127;ECNT=1;FS=0;HCNT=47;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=1.117;TLOD=4.43;ANN=G|frameshift_variant|HIGH|CTH|ENSG00000116761|transcript|ENST00000370938|protein_coding|1/12|c.12delA|p.Asp5fs|156/1805|12/1218|4/405||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|CTH|ENSG00000116761|transcript|ENST00000411986|protein_coding|1/11|c.12delA|p.Asp5fs|210/2044|12/1122|4/373||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|CTH|ENSG00000116761|transcript|ENST00000346806|protein_coding|1/11|c.12delA|p.Asp5fs|45/1196|12/1086|4/361||INFO_REALIGN_3_PRIME,G|non_coding_transcript_exon_variant|MODIFIER|CTH|ENSG00000116761|transcript|ENST00000464926|processed_transcript|1/6|n.156delA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:83,1:0.036:84 0/0:37,0:0:37 | |
| chr1 78410006 . AAT A . PASS ClippingRankSum=0;DP=308;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.03;ReadPosRankSum=-0.493;TLOD=25.61;ANN=A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000334785|protein_coding||c.*1493_*1494delAT|||||1098|,A|downstream_gene_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000436586|protein_coding||c.*4443_*4444delAT|||||4361|,A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000457030|protein_coding||c.*1409_*1410delAT|||||1409|,A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000330010|protein_coding||c.*1493_*1494delAT|||||431|,A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000342754|protein_coding||c.*1409_*1410delAT|||||427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000480732|processed_transcript||n.*1123_*1124delAT|||||1123|,A|downstream_gene_variant|MODIFIER|NEXN|ENSG00000162614|transcript|ENST00000470735|retained_intron||n.*1569_*1570delAT|||||1569|,A|downstream_gene_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000294623|nonsense_mediated_decay||c.*3191_*3192delAT|||||2160|,A|downstream_gene_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000370768|protein_coding||c.*4443_*4444delAT|||||4083|,A|downstream_gene_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000370767|protein_coding||c.*4550_*4551delAT|||||4083|,A|downstream_gene_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000487684|processed_transcript||n.*4647_*4648delAT|||||4648|,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000483894|processed_transcript|1/1|n.391-54_391-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000480673|processed_transcript|1/1|n.48-54_48-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000474632|processed_transcript|3/3|n.425-54_425-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000489495|processed_transcript|2/2|n.1942-54_1942-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000488814|processed_transcript|4/4|n.398-54_398-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000492405|processed_transcript|5/5|n.454-54_454-53delAT||||||,A|intron_variant|MODIFIER|FUBP1|ENSG00000162613|transcript|ENST00000492724|processed_transcript|3/3|n.369-54_369-53delAT|||||| GT:AD:AF:DP 0/1:184,23:0.103:207 0/0:73,5:0.054:78 | |
| chr1 81969063 . CCAG C . t_lod_fstar ClippingRankSum=0;DP=81;ECNT=1;FS=2.052;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=54.11;MQ0=4;MQRankSum=-1.769;NLOD=6.01;ReadPosRankSum=-0.211;TLOD=5.70;ANN=C|upstream_gene_variant|MODIFIER|RP5-837I24.6|ENSG00000227960|transcript|ENST00000439024|sense_intronic||n.-1720_-1718delCAG|||||1720|,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000473719|processed_transcript|2/4|n.419+58303_419+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370721|protein_coding|2/24|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370723|protein_coding|2/24|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370725|protein_coding|2/25|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370727|protein_coding|2/24|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370728|protein_coding|2/24|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000370730|protein_coding|2/23|c.-248+58303_-248+58305delAGC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|LPHN2|ENSG00000117114|transcript|ENST00000469377|processed_transcript|2/8|n.380+58303_380+58305delAGC||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|RP5-837I24.1|ENSG00000227288|transcript|ENST00000448213|processed_pseudogene|1/1|n.1599_1601delAGC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:42,4:0.059:46 0/0:27,0:0:27 | |
| chr1 86453265 . CTCT C . PASS ClippingRankSum=0;DP=536;ECNT=1;FS=0;HCNT=35;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.36;ReadPosRankSum=-0.08;TLOD=27.01;ANN=C|intron_variant|MODIFIER|COL24A1|ENSG00000171502|transcript|ENST00000370571|protein_coding|20/59|c.2364+16_2364+18delAGA||||||,C|intron_variant|MODIFIER|COL24A1|ENSG00000171502|transcript|ENST00000436319|protein_coding|20/57|c.2364+16_2364+18delAGA||||||,C|intron_variant|MODIFIER|COL24A1|ENSG00000171502|transcript|ENST00000426639|nonsense_mediated_decay|20/58|c.2364+16_2364+18delAGA|||||| GT:AD:AF:DP 0/1:345,14:0.042:359 0/0:137,8:0.059:145 | |
| chr1 87181439 . G T . t_lod_fstar ClippingRankSum=0;DP=82;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=-0.086;TLOD=4.55;ANN=T|missense_variant|MODERATE|SH3GLB1|ENSG00000097033|transcript|ENST00000482504|protein_coding|2/11|c.105G>T|p.Lys35Asn|110/1199|105/1161|35/386||,T|missense_variant|MODERATE|SH3GLB1|ENSG00000097033|transcript|ENST00000370558|protein_coding|2/9|c.105G>T|p.Lys35Asn|429/6371|105/1098|35/365||,T|intron_variant|MODIFIER|SH3GLB1|ENSG00000097033|transcript|ENST00000535010|protein_coding|1/7|c.-86-3751G>T|||||| GT:AD:AF:DP 0/1:51,1:0.051:52 0/0:30,0:0:30 | |
| chr1 90400152 . A G . t_lod_fstar ClippingRankSum=0;DP=235;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.76;ReadPosRankSum=1.846;TLOD=4.66;ANN=G|missense_variant|MODERATE|LRRC8D|ENSG00000171492|transcript|ENST00000337338|protein_coding|3/3|c.1525A>G|p.Ile509Val|1932/3950|1525/2577|509/858||,G|missense_variant|MODERATE|LRRC8D|ENSG00000171492|transcript|ENST00000394593|protein_coding|3/3|c.1525A>G|p.Ile509Val|1937/3345|1525/2577|509/858||,G|downstream_gene_variant|MODIFIER|RP11-302M6.4|ENSG00000271949|transcript|ENST00000370453|nonsense_mediated_decay||c.*90935A>G|||||1343|,G|downstream_gene_variant|MODIFIER|LRRC8D|ENSG00000171492|transcript|ENST00000525774|protein_coding||c.*1433A>G|||||1433|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|LRRC8D|ENSG00000171492|transcript|ENST00000532201|protein_coding||c.*1160A>G|||||1160|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|LRRC8D|ENSG00000171492|transcript|ENST00000414841|protein_coding||c.*1175A>G|||||1175|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|LRRC8D|ENSG00000171492|transcript|ENST00000527156|protein_coding||c.*965A>G|||||965|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|LRRC8D|ENSG00000171492|transcript|ENST00000441269|protein_coding||c.*701A>G|||||701|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:151,4:0.018:155 0/0:79,0:0:79 | |
| chr1 92516005 . GTAT G . t_lod_fstar ClippingRankSum=0;DP=515;ECNT=1;FS=0;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.22;ReadPosRankSum=-0.893;TLOD=4.17;ANN=G|intron_variant|MODIFIER|EPHX4|ENSG00000172031|transcript|ENST00000370383|protein_coding|5/6|c.708+43_708+45delTTA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:317,4:0.01:321 0/0:119,2:0.013:121 | |
| chr1 94335313 . G T . t_lod_fstar ClippingRankSum=0;DP=276;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.41;ReadPosRankSum=0.385;TLOD=4.08;ANN=T|3_prime_UTR_variant|MODIFIER|DNTTIP2|ENSG00000067334|transcript|ENST00000436063|protein_coding|7/7|c.*94C>A|||||94|,T|downstream_gene_variant|MODIFIER|DNTTIP2|ENSG00000067334|transcript|ENST00000462746|retained_intron||n.*23C>A|||||23|,T|downstream_gene_variant|MODIFIER|DNTTIP2|ENSG00000067334|transcript|ENST00000496535|processed_transcript||n.*23C>A|||||23|,T|downstream_gene_variant|MODIFIER|DNTTIP2|ENSG00000067334|transcript|ENST00000359208|nonsense_mediated_decay||c.*2437C>A|||||41| GT:AD:AF:DP 0/1:185,4:0.023:189 0/0:87,0:0:87 | |
| chr1 94955506 . A T . PASS ClippingRankSum=0;DP=154;ECNT=1;FS=6.791;HCNT=15;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.13;ReadPosRankSum=0.429;TLOD=74.15;ANN=T|missense_variant|MODERATE|ABCD3|ENSG00000117528|transcript|ENST00000454898|protein_coding|16/24|c.1369A>T|p.Ile457Phe|1435/2269|1369/2052|457/683||,T|missense_variant|MODERATE|ABCD3|ENSG00000117528|transcript|ENST00000394233|protein_coding|11/19|c.967A>T|p.Ile323Phe|1069/3286|967/1650|323/549||,T|missense_variant|MODERATE|ABCD3|ENSG00000117528|transcript|ENST00000536817|protein_coding|14/22|c.1078A>T|p.Ile360Phe|1324/2480|1078/1761|360/586||,T|missense_variant|MODERATE|ABCD3|ENSG00000117528|transcript|ENST00000370214|protein_coding|15/23|c.1297A>T|p.Ile433Phe|1321/3538|1297/1980|433/659||,T|downstream_gene_variant|MODIFIER|ABCD3|ENSG00000117528|transcript|ENST00000493416|processed_transcript||n.*2159A>T|||||2159|,T|non_coding_transcript_exon_variant|MODIFIER|ABCD3|ENSG00000117528|transcript|ENST00000484213|processed_transcript|6/14|n.2147A>T|||||| GT:AD:AF:DP 0/1:58,48:0.415:106 0/0:47,0:0:47 | |
| chr1 97145101 . C A . t_lod_fstar ClippingRankSum=0;DP=213;ECNT=1;FS=5.47;HCNT=25;MAX_ED=.;MIN_ED=.;MQ=58.82;MQ0=0;MQRankSum=-6.268;NLOD=7.69;ReadPosRankSum=-0.436;TLOD=4.40;ANN=A|non_coding_transcript_exon_variant|MODIFIER|RPL7P9|ENSG00000137970|transcript|ENST00000468715|processed_pseudogene|1/1|n.76G>T|||||| GT:AD:AF:DP 0/1:137,5:0.028:142 0/0:65,3:0.041:68 | |
| chr1 101197087 . G T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=12;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.20;ReadPosRankSum=-0.987;TLOD=5.20;ANN=T|upstream_gene_variant|MODIFIER|VCAM1|ENSG00000162692|transcript|ENST00000603679|retained_intron||n.-3644G>T|||||3644|,T|intron_variant|MODIFIER|VCAM1|ENSG00000162692|transcript|ENST00000294728|protein_coding|6/8|c.1525+13G>T||||||,T|intron_variant|MODIFIER|VCAM1|ENSG00000162692|transcript|ENST00000370119|protein_coding|6/8|c.1339+13G>T||||||,T|intron_variant|MODIFIER|VCAM1|ENSG00000162692|transcript|ENST00000347652|protein_coding|5/7|c.1249+13G>T||||||,T|intron_variant|MODIFIER|VCAM1|ENSG00000162692|transcript|ENST00000370115|protein_coding|4/6|c.929-887G>T|||||| GT:AD:AF:DP 0/1:6,2:0.25:8 0/0:4,0:0:4 | |
| chr1 101338183 . G T . t_lod_fstar ClippingRankSum=0;DP=259;ECNT=1;FS=4.216;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.24;ReadPosRankSum=1.293;TLOD=4.03;ANN=T|3_prime_UTR_variant|MODIFIER|EXTL2|ENSG00000162694|transcript|ENST00000370113|protein_coding|5/5|c.*1315C>A|||||1315|,T|3_prime_UTR_variant|MODIFIER|EXTL2|ENSG00000162694|transcript|ENST00000370114|protein_coding|5/5|c.*1315C>A|||||1315|,T|downstream_gene_variant|MODIFIER|EXTL2|ENSG00000162694|transcript|ENST00000535414|protein_coding||c.*1315C>A|||||929|,T|downstream_gene_variant|MODIFIER|EXTL2|ENSG00000162694|transcript|ENST00000450240|protein_coding||c.*1533C>A|||||1533|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|EXTL2|ENSG00000162694|transcript|ENST00000416479|protein_coding||c.*4892C>A|||||4892|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:186,5:0.023:191 0/0:67,0:0:67 | |
| chr1 103444316 . CAAGAA C . t_lod_fstar ClippingRankSum=0;DP=303;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.21;ReadPosRankSum=1.033;TLOD=4.50;ANN=C|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000358392|protein_coding|34/66|c.2746-13_2746-9delTTCTT||||||,C|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000370096|protein_coding|34/66|c.2710-13_2710-9delTTCTT||||||,C|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000353414|protein_coding|33/65|c.2593-13_2593-9delTTCTT||||||,C|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000512756|protein_coding|32/64|c.2362-13_2362-9delTTCTT|||||| GT:AD:AF:DP 0/1:170,3:0.015:173 0/0:94,0:0:94 | |
| chr1 103455020 . AAT A . PASS ClippingRankSum=0;DP=454;ECNT=1;FS=1.459;HCNT=15;MAX_ED=.;MIN_ED=.;MQ=60.07;MQ0=0;MQRankSum=7.905;NLOD=22.35;ReadPosRankSum=0.521;TLOD=22.22;ANN=A|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000358392|protein_coding|29/66|c.2430+52_2430+53delAT||||||,A|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000370096|protein_coding|29/66|c.2394+52_2394+53delAT||||||,A|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000353414|protein_coding|28/65|c.2277+52_2277+53delAT||||||,A|intron_variant|MODIFIER|COL11A1|ENSG00000060718|transcript|ENST00000512756|protein_coding|27/64|c.2046+52_2046+53delAT|||||| GT:AD:AF:DP 0/1:301,19:0.062:320 0/0:122,1:0.012:123 | |
| chr1 107867489 . G T . t_lod_fstar ClippingRankSum=0;DP=74;ECNT=1;FS=2.32;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=59.6;MQ0=0;MQRankSum=0;NLOD=5.12;ReadPosRankSum=0.167;TLOD=4.05;ANN=T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370068|protein_coding|3/8|c.832G>T|p.Glu278*|1678/4034|832/1620|278/539||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370071|protein_coding|3/8|c.832G>T|p.Glu278*|1550/3149|832/1443|278/480||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370073|protein_coding|3/8|c.832G>T|p.Glu278*|1550/3326|832/1620|278/539||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370074|protein_coding|3/6|c.832G>T|p.Glu278*|1550/3048|832/1317|278/438||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370061|protein_coding|3/8|c.832G>T|p.Glu278*|1540/2856|832/1518|278/505||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370070|protein_coding|3/8|c.832G>T|p.Glu278*|1540/2721|832/1383|278/460||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370072|protein_coding|3/8|c.832G>T|p.Glu278*|1540/2823|832/1485|278/494||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000542803|protein_coding|3/9|c.832G>T|p.Glu278*|1540/2958|832/1620|278/539||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370067|protein_coding|3/7|c.832G>T|p.Glu278*|1459/4628|832/1383|278/460||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370065|protein_coding|2/6|c.832G>T|p.Glu278*|832/1485|832/1485|278/494||,T|stop_gained|HIGH|NTNG1|ENSG00000162631|transcript|ENST00000370066|protein_coding|2/7|c.832G>T|p.Glu278*|832/1443|832/1443|278/480||,T|non_coding_transcript_exon_variant|MODIFIER|NTNG1|ENSG00000162631|transcript|ENST00000294649|retained_intron|3/5|n.1571G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NTNG1|ENSG00000162631|transcript|ENST00000477948|processed_transcript|2/5|n.800G>T||||||;LOF=(NTNG1|ENSG00000162631|15|0.73);NMD=(NTNG1|ENSG00000162631|15|0.73) GT:AD:AF:DP 0/1:47,3:0.059:50 0/0:23,0:0:23 | |
| chr1 109395267 . G T . t_lod_fstar ClippingRankSum=0;DP=121;ECNT=1;FS=0;HCNT=80;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.82;ReadPosRankSum=-1.141;TLOD=4.38;ANN=T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000370001|protein_coding|2/16|c.20C>A|p.Ser7*|289/3053|20/2511|7/836||,T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000474186|nonsense_mediated_decay|3/14|c.20C>A|p.Ser7*|426/2895|20/1959|7/652||,T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000369994|protein_coding|1/13|c.20C>A|p.Ser7*|73/2318|20/2169|7/722||,T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000369995|protein_coding|2/14|c.20C>A|p.Ser7*|279/2641|20/2286|7/761||,T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000461774|nonsense_mediated_decay|2/12|c.20C>A|p.Ser7*|271/2646|20/1710|7/569||,T|stop_gained|HIGH|AKNAD1|ENSG00000162641|transcript|ENST00000472781|nonsense_mediated_decay|2/7|c.20C>A|p.Ser7*|279/2638|20/1248|7/415||,T|upstream_gene_variant|MODIFIER|SPATA42|ENSG00000203897|transcript|ENST00000369989|antisense||n.-4572G>T|||||4572|,T|upstream_gene_variant|MODIFIER|SPATA42|ENSG00000203897|transcript|ENST00000417241|antisense||n.-4599G>T|||||4599|,T|intron_variant|MODIFIER|AKNAD1|ENSG00000162641|transcript|ENST00000357393|protein_coding|1/11|c.115-3069C>A||||||;LOF=(AKNAD1|ENSG00000162641|10|0.60);NMD=(AKNAD1|ENSG00000162641|10|0.60) GT:AD:AF:DP 0/1:80,4:0.033:84 0/0:37,0:0:37 | |
| chr1 109944649 . T C . PASS ClippingRankSum=0;DP=156;ECNT=1;FS=4.834;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.42;ReadPosRankSum=0.965;TLOD=126.13;ANN=C|missense_variant|MODERATE|PSMA5|ENSG00000143106|transcript|ENST00000271308|protein_coding|9/9|c.712A>G|p.Ile238Val|733/3729|712/726|238/241||,C|missense_variant|MODERATE|PSMA5|ENSG00000143106|transcript|ENST00000538610|protein_coding|8/8|c.538A>G|p.Ile180Val|755/985|538/552|180/183||,C|upstream_gene_variant|MODIFIER|SORT1|ENSG00000134243|transcript|ENST00000256637|protein_coding||c.-4135A>G|||||4076|,C|upstream_gene_variant|MODIFIER|SORT1|ENSG00000134243|transcript|ENST00000471996|processed_transcript||n.-4166A>G|||||4166|,C|non_coding_transcript_exon_variant|MODIFIER|PSMA5|ENSG00000143106|transcript|ENST00000490870|processed_transcript|9/9|n.1490A>G|||||| GT:AD:AF:DP 0/1:51,65:0.6:116 0/0:39,0:0:39 | |
| chr1 110256127 . G A . PASS ClippingRankSum=0;DP=125;ECNT=1;FS=15.601;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=58.59;MQ0=1;MQRankSum=-8.825;NLOD=9.63;ReadPosRankSum=-2.175;TLOD=8.59;ANN=A|missense_variant|MODERATE|GSTM5|ENSG00000134201|transcript|ENST00000369812|protein_coding|4/8|c.256G>A|p.Ala86Thr|327/1625|256/714|86/237||,A|missense_variant|MODERATE|GSTM5|ENSG00000134201|transcript|ENST00000256593|protein_coding|4/8|c.199G>A|p.Ala67Thr|257/1555|199/657|67/218||,A|missense_variant|MODERATE|GSTM5|ENSG00000134201|transcript|ENST00000369813|protein_coding|2/5|c.76G>A|p.Ala26Thr|981/4370|76/609|26/202||,A|upstream_gene_variant|MODIFIER|GSTM5|ENSG00000134201|transcript|ENST00000492718|processed_transcript||n.-39G>A|||||39|,A|upstream_gene_variant|MODIFIER|GSTM5|ENSG00000134201|transcript|ENST00000483153|processed_transcript||n.-1111G>A|||||1111|,A|downstream_gene_variant|MODIFIER|GSTM2|ENSG00000213366|transcript|ENST00000369831|protein_coding||c.*4929G>A|||||3956|,A|downstream_gene_variant|MODIFIER|GSTM1|ENSG00000134184|transcript|ENST00000490021|processed_transcript||n.*4466G>A|||||4466|,A|downstream_gene_variant|MODIFIER|GSTM1|ENSG00000134184|transcript|ENST00000483399|protein_coding||c.*24200G>A|||||4820|,A|intron_variant|MODIFIER|GSTM5|ENSG00000134201|transcript|ENST00000429410|processed_transcript|1/1|n.82+1157G>A|||||| GT:AD:AF:DP 0/1:73,5:0.089:78 0/0:45,0:0:45 | |
| chr1 110596581 . G T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=31;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.11;ReadPosRankSum=-0.268;TLOD=4.13;ANN=T|3_prime_UTR_variant|MODIFIER|STRIP1|ENSG00000143093|transcript|ENST00000369795|protein_coding|21/21|c.*47G>T|||||47|,T|3_prime_UTR_variant|MODIFIER|STRIP1|ENSG00000143093|transcript|ENST00000369796|protein_coding|21/21|c.*47G>T|||||47|,T|3_prime_UTR_variant|MODIFIER|STRIP1|ENSG00000143093|transcript|ENST00000485775|nonsense_mediated_decay|22/22|c.*2036G>T|||||14078|,T|upstream_gene_variant|MODIFIER|RP4-773N10.4|ENSG00000258634|transcript|ENST00000554749|antisense||n.-4381G>T|||||4381|,T|non_coding_transcript_exon_variant|MODIFIER|STRIP1|ENSG00000143093|transcript|ENST00000473429|retained_intron|12/14|n.3370G>T|||||| GT:AD:AF:DP 0/1:21,3:0.111:24 0/0:7,0:0:7 | |
| chr1 115537499 . TCAGGCCCC T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=286;ECNT=4;FS=12.688;HCNT=24;MAX_ED=14;MIN_ED=10;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.12;ReadPosRankSum=1.904;TLOD=7.04;ANN=T|frameshift_variant&splice_acceptor_variant&splice_region_variant&intron_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369518|protein_coding|32/32|c.2794-3_2798delCAGGCCCC|p.Ala932fs||2794/2931|932/976||,T|frameshift_variant&splice_acceptor_variant&splice_region_variant&intron_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369522|protein_coding|32/32|c.2794-3_2798delCAGGCCCC|p.Ala932fs||2794/2931|932/976||,T|splice_acceptor_variant&splice_region_variant&intron_variant&non_coding_transcript_exon_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000477590|processed_transcript|4/4|n.328-3_332delCAGGCCCC|||||| GT:AD:AF:DP:PGT:PID 0/1:200,5:0.019:205:0|1:115537499_TCAGGCCCC_T 0/0:72,3:0.048:75:0|1:115537499_TCAGGCCCC_T | |
| chr1 115537509 . TCA T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=223;ECNT=4;FS=15.592;HCNT=25;MAX_ED=14;MIN_ED=10;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.15;TLOD=7.26;ANN=T|frameshift_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369518|protein_coding|32/32|c.2801_2802delCA|p.Ser934fs|2974/3452|2801/2931|934/976||,T|frameshift_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369522|protein_coding|32/32|c.2801_2802delCA|p.Ser934fs|3041/3522|2801/2931|934/976||,T|non_coding_transcript_exon_variant|MODIFIER|SYCP1|ENSG00000198765|transcript|ENST00000477590|processed_transcript|4/4|n.335_336delCA|||||| GT:AD:AF:DP 0/1:159,5:0.022:164 0/0:55,3:0.058:58 | |
| chr1 115537511 . A ATTTTTTTTTT . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=215;ECNT=4;FS=15.904;HCNT=24;MAX_ED=14;MIN_ED=10;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.55;TLOD=7.31;ANN=ATTTTTTTTTT|frameshift_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369518|protein_coding|32/32|c.2803_2804insTTTTTTTTTT|p.Ser935fs|2977/3452|2804/2931|935/976||INFO_REALIGN_3_PRIME,ATTTTTTTTTT|frameshift_variant|HIGH|SYCP1|ENSG00000198765|transcript|ENST00000369522|protein_coding|32/32|c.2803_2804insTTTTTTTTTT|p.Ser935fs|3044/3522|2804/2931|935/976||INFO_REALIGN_3_PRIME,ATTTTTTTTTT|non_coding_transcript_exon_variant|MODIFIER|SYCP1|ENSG00000198765|transcript|ENST00000477590|processed_transcript|4/4|n.337_338insTTTTTTTTTT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:152,5:0.023:157:0|1:115537499_TCAGGCCCC_T 0/0:54,3:0.06:57:0|1:115537499_TCAGGCCCC_T | |
| chr1 115537513 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=208;ECNT=4;FS=16.011;HCNT=24;MAX_ED=14;MIN_ED=10;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.55;ReadPosRankSum=0.229;TLOD=7.37;ANN=T|missense_variant|MODERATE|SYCP1|ENSG00000198765|transcript|ENST00000369518|protein_coding|32/32|c.2804C>T|p.Ser935Phe|2977/3452|2804/2931|935/976||,T|missense_variant|MODERATE|SYCP1|ENSG00000198765|transcript|ENST00000369522|protein_coding|32/32|c.2804C>T|p.Ser935Phe|3044/3522|2804/2931|935/976||,T|non_coding_transcript_exon_variant|MODIFIER|SYCP1|ENSG00000198765|transcript|ENST00000477590|processed_transcript|4/4|n.338C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:148,5:0.024:153:0|1:115537499_TCAGGCCCC_T 0/0:51,3:0.06:54:0|1:115537499_TCAGGCCCC_T | |
| chr1 117626789 . G T . t_lod_fstar ClippingRankSum=0;DP=144;ECNT=1;FS=2.567;HCNT=42;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=-1.081;TLOD=5.22;ANN=T|missense_variant&splice_region_variant|MODERATE|TTF2|ENSG00000116830|transcript|ENST00000369466|protein_coding|11/23|c.2053G>T|p.Val685Phe|2097/9462|2053/3489|685/1162|| GT:AD:AF:DP 0/1:110,3:0.038:113 0/0:30,0:0:30 | |
| chr1 117654900 . A G . t_lod_fstar ClippingRankSum=0;DP=95;ECNT=1;FS=1.887;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=0.844;TLOD=4.20;ANN=G|3_prime_UTR_variant|MODIFIER|TRIM45|ENSG00000134253|transcript|ENST00000256649|protein_coding|6/6|c.*27T>C|||||27|,G|3_prime_UTR_variant|MODIFIER|TRIM45|ENSG00000134253|transcript|ENST00000497970|nonsense_mediated_decay|3/4|c.*27T>C|||||27|WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|TRIM45|ENSG00000134253|transcript|ENST00000369464|protein_coding|6/6|c.*27T>C|||||27|,G|3_prime_UTR_variant|MODIFIER|TRIM45|ENSG00000134253|transcript|ENST00000369461|protein_coding|7/7|c.*27T>C|||||27|,G|downstream_gene_variant|MODIFIER|TTF2|ENSG00000116830|transcript|ENST00000369466|protein_coding||c.*10754A>G|||||4825| GT:AD:AF:DP 0/1:64,4:0.064:68 0/0:27,0:0:27 | |
| chr1 120612034 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=191;ECNT=2;FS=1.128;HCNT=17;MAX_ED=6;MIN_ED=6;MQ=51.03;MQ0=0;MQRankSum=-4.101;NLOD=11.64;ReadPosRankSum=-1.038;TLOD=13.86;ANN=G|5_prime_UTR_variant|MODIFIER|NOTCH2|ENSG00000134250|transcript|ENST00000256646|protein_coding|1/34|c.-14A>C|||||14|,G|non_coding_transcript_exon_variant|MODIFIER|NOTCH2|ENSG00000134250|transcript|ENST00000479412|retained_intron|1/14|n.207A>C|||||| GT:AD:AF:DP 0/1:107,13:0.121:120 0/0:56,1:0.022:57 | |
| chr1 120612040 . T TCCGCCGCCG . clustered_events;multi_event_alt_allele_in_normal;triallelic_site ClippingRankSum=0;DP=222;ECNT=2;FS=0;HCNT=10;MAX_ED=6;MIN_ED=6;MQ=50.8;MQ0=0;MQRankSum=-5.161;NLOD=5.46;ReadPosRankSum=0.64;TLOD=58.67;ANN=TCCGCCGCCG|5_prime_UTR_variant|MODIFIER|NOTCH2|ENSG00000134250|transcript|ENST00000256646|protein_coding|1/34|c.-29_-21dupCGGCGGCGG|||||21|,TCCGCCGCCG|non_coding_transcript_exon_variant|MODIFIER|NOTCH2|ENSG00000134250|transcript|ENST00000479412|retained_intron|1/14|n.192_200dupCGGCGGCGG|||||| GT:AD:AF:DP 0/1:95,30:0.177:125 0/0:46,8:0:54 | |
| chr1 121137569 . T C . germline_risk;t_lod_fstar ClippingRankSum=0;DP=128;ECNT=1;FS=1.104;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=47.2;MQ0=21;MQRankSum=0.289;NLOD=1.59;ReadPosRankSum=-0.033;TLOD=4.46;ANN=C|upstream_gene_variant|MODIFIER|AL592494.5|ENSG00000227082|transcript|ENST00000417218|lincRNA||n.-1045T>C|||||1045|,C|downstream_gene_variant|MODIFIER|RP11-343N15.5|ENSG00000269996|transcript|ENST00000602412|lincRNA||n.*2988T>C|||||2988|,C|downstream_gene_variant|MODIFIER|RP11-343N15.1|ENSG00000230806|transcript|ENST00000429055|lincRNA||n.*1769A>G|||||1769|,C|intron_variant|MODIFIER|RP11-343N15.1|ENSG00000230806|transcript|ENST00000437515|lincRNA|2/3|n.329+1772A>G|||||| GT:AD:AF:DP 0/1:64,5:0.071:69 0/0:26,9:0.261:35 | |
| chr1 142690664 . G C . PASS ClippingRankSum=0;DP=1010;ECNT=1;FS=0;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=36.18;MQ0=502;MQRankSum=-0.957;NLOD=7.85;ReadPosRankSum=0.304;TLOD=9.61;ANN=C|upstream_gene_variant|MODIFIER|SNX18P16|ENSG00000233218|transcript|ENST00000417988|processed_pseudogene||n.-1739C>G|||||1739|,C|intron_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|11/13|n.3560+2298C>G||||||,C|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000446205|lincRNA|4/5|n.401-200G>C||||||,C|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-33515G>C||||||,C|intron_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|6/8|n.2507+2298C>G|||||| GT:AD:AF:DP 0/1:176,10:0.047:186 0/0:241,12:0.051:253 | |
| chr1 142700046 . G A . PASS ClippingRankSum=0;DP=1896;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=38.08;MQ0=867;MQRankSum=-6.012;NLOD=52.62;ReadPosRankSum=-0.743;TLOD=126.21;ANN=A|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-24133G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|8/14|n.3121C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|9/11|n.1949C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|3/9|n.2068C>T|||||| GT:AD:AF:DP 0/1:448,71:0.139:519 0/0:444,0:0:444 | |
| chr1 142700204 . A C . t_lod_fstar ClippingRankSum=0;DP=799;ECNT=1;FS=6.671;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=40.92;MQ0=160;MQRankSum=4.165;NLOD=6.30;ReadPosRankSum=-3.463;TLOD=4.99;ANN=C|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-23975A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|8/14|n.2963T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|9/11|n.1791T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|3/9|n.1910T>G|||||| GT:AD:AF:DP 0/1:397,3:0.011:400 0/0:198,18:0.084:216 | |
| chr1 142711339 . G A . PASS ClippingRankSum=0;DP=1379;ECNT=1;FS=4.296;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=48.19;MQ0=50;MQRankSum=1.979;NLOD=8.79;ReadPosRankSum=-1.444;TLOD=10.20;ANN=A|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*3824C>T|||||3824|,A|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-12840G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|7/14|n.2768C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|8/11|n.1596C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|2/9|n.1715C>T|||||| GT:AD:AF:DP 0/1:917,11:0.015:928 0/0:296,23:0.082:319 | |
| chr1 142713119 . C T . PASS ClippingRankSum=0;DP=1162;ECNT=1;FS=12.285;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=42.77;MQ0=257;MQRankSum=-1.174;NLOD=17.22;ReadPosRankSum=-7.74;TLOD=27.48;ANN=T|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*2044G>A|||||2044|,T|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-11060C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.2540G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.1364G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.1487G>A|||||| GT:AD:AF:DP 0/1:585,23:0.054:608 0/0:245,26:0.106:271 | |
| chr1 142713555 . T TAA . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=632;ECNT=2;FS=47.816;HCNT=18;MAX_ED=53;MIN_ED=53;MQ=36.08;MQ0=217;MQRankSum=-1.33;NLOD=8.78;ReadPosRankSum=-0.482;TLOD=49.57;ANN=TAA|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*1607_*1608insTT|||||1607|,TAA|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-10624_517-10623insAA||||||,TAA|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.2103_2104insTT||||||,TAA|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.927_928insTT||||||,TAA|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.1050_1051insTT|||||| GT:AD:AF:DP 0/1:225,16:0.084:241 0/0:136,10:0.095:146 | |
| chr1 142713608 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1086;ECNT=2;FS=3.142;HCNT=23;MAX_ED=53;MIN_ED=53;MQ=34.54;MQ0=440;MQRankSum=-2.191;NLOD=2.63;ReadPosRankSum=-1.314;TLOD=52.53;ANN=T|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*1555G>A|||||1555|,T|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-10571C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.2051G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.875G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.998G>A|||||| GT:AD:AF:DP 0/1:292,40:0.115:332 0/0:235,26:0.082:261 | |
| chr1 142713724 . G GTT . clustered_events;homologous_mapping_event;triallelic_site ClippingRankSum=0;DP=998;ECNT=3;FS=3.515;HCNT=14;MAX_ED=50;MIN_ED=49;MQ=49.19;MQ0=108;MQRankSum=-8.454;NLOD=36.78;ReadPosRankSum=-0.935;TLOD=11.61;ANN=GTT|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*1437_*1438dupAA|||||1438|,GTT|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-10449_517-10448dupTT||||||INFO_REALIGN_3_PRIME,GTT|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.1933_1934dupAA||||||,GTT|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.757_758dupAA||||||,GTT|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.880_881dupAA|||||| GT:AD:AF:DP 0/1:523,29:0.045:552 0/0:199,0:0:199 | |
| chr1 142713773 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=748;ECNT=3;FS=0;HCNT=14;MAX_ED=50;MIN_ED=49;MQ=58.96;MQ0=10;MQRankSum=-5.935;NLOD=5.95;ReadPosRankSum=0.886;TLOD=7.12;ANN=G|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*1390G>C|||||1390|,G|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-10406C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.1886G>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.710G>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.833G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:557,4:0.01:561:0|1:142713773_C_G 0/0:154,13:0.102:167:0|1:142713773_C_G | |
| chr1 142713774 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=745;ECNT=3;FS=0;HCNT=14;MAX_ED=50;MIN_ED=49;MQ=59.11;MQ0=10;MQRankSum=-5.241;NLOD=6.26;ReadPosRankSum=1.292;TLOD=7.12;ANN=G|downstream_gene_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000595144|lincRNA||n.*1389T>C|||||1389|,G|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|2/3|n.517-10405A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|6/14|n.1885T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|7/11|n.709T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000369381|lincRNA|1/9|n.832T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:559,3:0.01:562:0|1:142713773_C_G 0/0:152,13:0.102:165:0|1:142713773_C_G | |
| chr1 142726970 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1618;ECNT=2;FS=5.99;HCNT=4;MAX_ED=48;MIN_ED=48;MQ=59.02;MQ0=17;MQRankSum=-3.827;NLOD=50.01;ReadPosRankSum=2.268;TLOD=5.92;ANN=G|splice_region_variant&intron_variant|LOW|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|2/13|n.112-8T>C||||||,G|splice_region_variant&intron_variant|LOW|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|2/10|n.116-8T>C||||||,G|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|3/3|n.604+2704A>G|||||| GT:AD:AF:DP 0/1:1186,9:0.009938:1195 0/0:367,28:0.079:395 | |
| chr1 142727018 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1985;ECNT=2;FS=4.68;HCNT=6;MAX_ED=48;MIN_ED=48;MQ=52.07;MQ0=216;MQRankSum=-4.373;NLOD=2.35;ReadPosRankSum=-1.806;TLOD=35.96;ANN=A|intron_variant|MODIFIER|RP11-417J8.6|ENSG00000203849|transcript|ENST00000610091|lincRNA|2/13|n.111+36C>T||||||,A|intron_variant|MODIFIER|ANKRD20A12P|ENSG00000242676|transcript|ENST00000416817|transcribed_unprocessed_pseudogene|2/10|n.115+36C>T||||||,A|intron_variant|MODIFIER|RP11-417J8.3|ENSG00000230880|transcript|ENST00000411746|lincRNA|3/3|n.604+2752G>A|||||| GT:AD:AF:DP 0/1:1215,42:0.032:1257 0/0:424,53:0.111:477 | |
| chr1 142797328 . T A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=903;ECNT=2;FS=6.589;HCNT=4;MAX_ED=23;MIN_ED=23;MQ=56.82;MQ0=12;MQRankSum=-3.423;NLOD=44.47;ReadPosRankSum=-3.282;TLOD=5.41;ANN=A|upstream_gene_variant|MODIFIER|ASNSP5|ENSG00000229683|transcript|ENST00000433327|unprocessed_pseudogene||n.-2259T>A|||||2259|,A|downstream_gene_variant|MODIFIER|RP11-423O2.1|ENSG00000230255|transcript|ENST00000458414|unprocessed_pseudogene||n.*4772T>A|||||4772|,A|intergenic_region|MODIFIER|RP11-423O2.1-ASNSP5|ENSG00000230255-ENSG00000229683|intergenic_region|ENSG00000230255-ENSG00000229683|||n.142797328T>A|||||| GT:AD:AF:DP 0/1:605,6:0.015:611 0/0:258,5:0.022:263 | |
| chr1 142797351 . A T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=948;ECNT=2;FS=0;HCNT=22;MAX_ED=23;MIN_ED=23;MQ=57.51;MQ0=8;MQRankSum=-7.771;NLOD=24.56;ReadPosRankSum=-1.825;TLOD=31.42;ANN=T|upstream_gene_variant|MODIFIER|ASNSP5|ENSG00000229683|transcript|ENST00000433327|unprocessed_pseudogene||n.-2236A>T|||||2236|,T|downstream_gene_variant|MODIFIER|RP11-423O2.1|ENSG00000230255|transcript|ENST00000458414|unprocessed_pseudogene||n.*4795A>T|||||4795|,T|intergenic_region|MODIFIER|RP11-423O2.1-ASNSP5|ENSG00000230255-ENSG00000229683|intergenic_region|ENSG00000230255-ENSG00000229683|||n.142797351A>T|||||| GT:AD:AF:DP 0/1:618,27:0.052:645 0/0:269,17:0.057:286 | |
| chr1 142803580 . TA T . PASS ClippingRankSum=0;DP=3537;ECNT=1;FS=1.006;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=45.28;MQ0=222;MQRankSum=-6.057;NLOD=86.53;ReadPosRankSum=0.185;TLOD=144.09;ANN=T|downstream_gene_variant|MODIFIER|ASNSP5|ENSG00000229683|transcript|ENST00000433327|unprocessed_pseudogene||n.*3842delA|||||3842|,T|intron_variant|MODIFIER|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|1/8|n.31+24delA||||||INFO_REALIGN_3_PRIME,T|non_coding_transcript_exon_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|3/3|n.1385delT|||||| GT:AD:AF:DP 0/1:1879,197:0.089:2076 0/0:988,66:0.056:1054 | |
| chr1 142813098 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=7033;ECNT=6;FS=0;HCNT=3;MAX_ED=86;MIN_ED=29;MQ=41.17;MQ0=924;MQRankSum=6.187;NLOD=287.40;ReadPosRankSum=2.23;TLOD=12.17;ANN=C|splice_region_variant&intron_variant|LOW|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|3/8|n.258-3T>C||||||,C|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2819A>G|||||| GT:AD:AF:DP 0/1:3727,40:0.015:3767 0/0:1820,116:0.063:1936 | |
| chr1 142813127 . A T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=-0;DP=7537;ECNT=6;FS=6.311;HCNT=5;MAX_ED=86;MIN_ED=29;MQ=41.29;MQ0=879;MQRankSum=-3.627;NLOD=337.33;ReadPosRankSum=-0.63;TLOD=72.68;ANN=T|splice_region_variant&non_coding_transcript_exon_variant|LOW|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|4/9|n.284A>T||||||,T|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2790T>A|||||| GT:AD:AF:DP 0/1:4060,74:0.023:4134 0/0:2144,29:0.015:2173 | |
| chr1 142813129 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=-0;DP=7522;ECNT=6;FS=15.847;HCNT=8;MAX_ED=86;MIN_ED=29;MQ=41.31;MQ0=859;MQRankSum=-3.766;NLOD=216.75;ReadPosRankSum=0.956;TLOD=245.39;ANN=A|splice_region_variant&non_coding_transcript_exon_variant|LOW|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|4/9|n.286G>A||||||,A|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2788C>T|||||| GT:AD:AF:DP 0/1:3961,142:0.048:4103 0/0:2097,75:0.039:2172 | |
| chr1 142813141 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=-0;DP=7536;ECNT=6;FS=0;HCNT=4;MAX_ED=86;MIN_ED=29;MQ=41.3;MQ0=893;MQRankSum=2.734;NLOD=298.74;ReadPosRankSum=-6.79;TLOD=9.63;ANN=C|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2776A>G||||||,C|intron_variant|MODIFIER|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|4/8|n.286+12T>C|||||| GT:AD:AF:DP 0/1:4011,29:0.008226:4040 0/0:2117,45:0.024:2162 | |
| chr1 142813165 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=-0;DP=7378;ECNT=6;FS=0;HCNT=3;MAX_ED=86;MIN_ED=29;MQ=41.08;MQ0=980;MQRankSum=3.975;NLOD=265.07;ReadPosRankSum=-0.363;TLOD=27.39;ANN=T|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2752G>A||||||,T|intron_variant|MODIFIER|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|4/8|n.286+36C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:3818,25:0.006939:3843:0|1:142813165_C_T 0/0:2110,61:0.028:2171:0|1:142813165_C_T | |
| chr1 142813184 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=7159;ECNT=6;FS=0;HCNT=3;MAX_ED=86;MIN_ED=29;MQ=40.93;MQ0=1044;MQRankSum=4.263;NLOD=259.35;ReadPosRankSum=0.284;TLOD=26.05;ANN=G|intron_variant|MODIFIER|RP11-423O2.5|ENSG00000234978|transcript|ENST00000423385|lincRNA|1/2|n.88+2733T>C||||||,G|intron_variant|MODIFIER|ANKRD20A14P|ENSG00000232745|transcript|ENST00000457776|unprocessed_pseudogene|4/8|n.287-37A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:3610,28:0.007308:3638:0|1:142813165_C_T 0/0:2052,71:0.029:2123:0|1:142813165_C_T | |
| chr1 143163798 . T G . PASS ClippingRankSum=0;DP=390;ECNT=1;FS=14.07;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=49.61;MQ0=39;MQRankSum=-2.869;NLOD=14.51;ReadPosRankSum=1.855;TLOD=10.24;ANN=G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+25636A>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.59+44679T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.4|ENSG00000237291|transcript|ENST00000424474|lincRNA|1/1|n.380-5694T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+30324A>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.59+44679T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.59+44679T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|MIR3118-2|ENSG00000265661|transcript|ENST00000582397|miRNA|1/1|n.49T>G|||||| GT:AD:AF:DP 0/1:225,8:0.049:233 0/0:99,4:0.039:103 | |
| chr1 143187147 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=176;ECNT=3;FS=20.019;HCNT=8;MAX_ED=25;MIN_ED=9;MQ=59.32;MQ0=2;MQRankSum=-8.069;NLOD=8.74;ReadPosRankSum=1.5;TLOD=6.78;ANN=T|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1681C>T|||||1681|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1362G>A|||||1362|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1362G>A|||||1362|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1648G>A|||||1648|,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+2287G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33487C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6975G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33487C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-44132C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-211G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:120,3:0.031:123:0|1:143187147_C_T 0/0:50,1:0.023:51:0|1:143187147_C_T | |
| chr1 143187156 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=202;ECNT=3;FS=19.802;HCNT=8;MAX_ED=25;MIN_ED=9;MQ=59.36;MQ0=2;MQRankSum=-9.438;NLOD=11.45;ReadPosRankSum=1.696;TLOD=8.12;ANN=G|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1672T>G|||||1672|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1353A>C|||||1353|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1353A>C|||||1353|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1639A>C|||||1639|,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+2278A>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33478T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6966A>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33478T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-44123T>G||||||,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-220A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:136,3:0.039:139:0|1:143187147_C_T 0/0:60,1:0.019:61:0|1:143187147_C_T | |
| chr1 143187172 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=253;ECNT=3;FS=19.66;HCNT=8;MAX_ED=25;MIN_ED=9;MQ=58.56;MQ0=3;MQRankSum=-5.448;NLOD=14.76;ReadPosRankSum=1.019;TLOD=4.91;ANN=G|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1656A>G|||||1656|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1337T>C|||||1337|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1337T>C|||||1337|,G|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1623T>C|||||1623|,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+2262T>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33462A>G||||||,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6950T>C||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33462A>G||||||,G|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-44107A>G||||||,G|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-236T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:164,3:0.025:167:0|1:143187147_C_T 0/0:80,1:0.016:81:0|1:143187147_C_T | |
| chr1 143187429 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=200;ECNT=4;FS=27.575;HCNT=8;MAX_ED=21;MIN_ED=4;MQ=53.69;MQ0=3;MQRankSum=-3.663;NLOD=9.62;ReadPosRankSum=-2.167;TLOD=9.79;ANN=A|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1399G>A|||||1399|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1080C>T|||||1080|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1080C>T|||||1080|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1366C>T|||||1366|,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+2005C>T||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33205G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6693C>T||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33205G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-43850G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-493C>T|||||| GT:AD:AF:DP 0/1:123,8:0.075:131 0/0:58,2:0.021:60 | |
| chr1 143187433 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=196;ECNT=4;FS=5.096;HCNT=10;MAX_ED=21;MIN_ED=4;MQ=53.16;MQ0=3;MQRankSum=-2.281;NLOD=8.44;ReadPosRankSum=-0.843;TLOD=9.57;ANN=A|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1395G>A|||||1395|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1076C>T|||||1076|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1076C>T|||||1076|,A|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1362C>T|||||1362|,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+2001C>T||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33201G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6689C>T||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33201G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-43846G>A||||||,A|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-497C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:126,3:0.04:129:0|1:143187433_G_A 0/0:56,1:0.022:57:0|1:143187433_G_A | |
| chr1 143187435 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=197;ECNT=4;FS=7.875;HCNT=10;MAX_ED=21;MIN_ED=4;MQ=52.96;MQ0=3;MQRankSum=-2.488;NLOD=8.44;ReadPosRankSum=-1.406;TLOD=9.54;ANN=T|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1393C>T|||||1393|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1074G>A|||||1074|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1074G>A|||||1074|,T|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1360G>A|||||1360|,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+1999G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33199C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6687G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33199C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-43844C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-499G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:124,4:0.039:128:0|1:143187433_G_A 0/0:57,1:0.021:58:0|1:143187433_G_A | |
| chr1 143187450 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=196;ECNT=4;FS=13.415;HCNT=16;MAX_ED=21;MIN_ED=4;MQ=51.72;MQ0=3;MQRankSum=-2.824;NLOD=5.68;ReadPosRankSum=-1.895;TLOD=12.55;ANN=C|upstream_gene_variant|MODIFIER|RP11-782C8.3|ENSG00000232336|transcript|ENST00000425124|lincRNA||n.-1378T>C|||||1378|,C|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.*1059A>G|||||1059|,C|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA||n.*1059A>G|||||1059|,C|downstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA||n.*1345A>G|||||1345|,C|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|6/8|n.2503+1984A>G||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-33184T>C||||||,C|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA|2/2|n.253+6672A>G||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-33184T>C||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-43829T>C||||||,C|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA|2/3|n.239-514A>G|||||| GT:AD:AF:DP 0/1:118,8:0.083:126 0/0:55,2:0.047:57 | |
| chr1 143196556 . T A . PASS ClippingRankSum=0;DP=1592;ECNT=1;FS=14.327;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=29.18;MQ0=1063;MQRankSum=-2.93;NLOD=3.86;ReadPosRankSum=-0.317;TLOD=11.85;ANN=A|upstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000422129|lincRNA||n.-845A>T|||||845|,A|upstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000437267|lincRNA||n.-2317A>T|||||2317|,A|upstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000420598|lincRNA||n.-722A>T|||||722|,A|upstream_gene_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000452738|lincRNA||n.-670A>T|||||670|,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-24078T>A||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-24078T>A||||||,A|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-34723T>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|3/9|n.2039A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000413897|lincRNA|1/6|n.248A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000447389|lincRNA|1/4|n.248A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000435913|lincRNA|1/2|n.248A>T|||||| GT:AD:AF:DP 0/1:114,8:0.066:122 0/0:321,7:0.031:328 | |
| chr1 143207696 . TA T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=945;ECNT=4;FS=0;HCNT=20;MAX_ED=30;MIN_ED=14;MQ=37.65;MQ0=297;MQRankSum=1.972;NLOD=45.45;ReadPosRankSum=0.924;TLOD=6.30;ANN=T|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000437865|retained_intron||n.*3931delT|||||3931|,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|2/8|n.1791+30delT||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-12936delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-12936delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-23581delA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:363,3:0.011:366:0|1:143207696_TA_T 0/0:249,11:0.044:260:0|1:143207696_TA_T | |
| chr1 143207710 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=946;ECNT=4;FS=0;HCNT=20;MAX_ED=30;MIN_ED=14;MQ=38.92;MQ0=270;MQRankSum=1.975;NLOD=46.66;ReadPosRankSum=-0.06;TLOD=6.26;ANN=T|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000437865|retained_intron||n.*3918G>A|||||3918|,T|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|2/8|n.1791+17G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-12924C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-12924C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-23569C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:385,3:0.01:388:0|1:143207696_TA_T 0/0:260,11:0.042:271:0|1:143207696_TA_T | |
| chr1 143207715 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=958;ECNT=4;FS=0;HCNT=20;MAX_ED=30;MIN_ED=14;MQ=39.34;MQ0=263;MQRankSum=2.005;NLOD=46.36;ReadPosRankSum=-0.318;TLOD=6.23;ANN=C|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000437865|retained_intron||n.*3913A>G|||||3913|,C|intron_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|2/8|n.1791+12A>G||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-12919T>C||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-12919T>C||||||,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-23564T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:402,3:0.01:405:0|1:143207696_TA_T 0/0:264,11:0.043:275:0|1:143207696_TA_T | |
| chr1 143207726 . CT C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=947;ECNT=4;FS=0;HCNT=20;MAX_ED=30;MIN_ED=14;MQ=40.05;MQ0=236;MQRankSum=1.037;NLOD=46.64;ReadPosRankSum=0.714;TLOD=6.17;ANN=C|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|2/9|n.1791delA||||||,C|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000437865|retained_intron||n.*3901delA|||||3901|,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-12906delT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-12906delT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-23551delT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:423,3:0.00974:426:0|1:143207696_TA_T 0/0:264,7:0.033:271:0|1:143207696_TA_T | |
| chr1 143209570 . C T . t_lod_fstar ClippingRankSum=0;DP=1557;ECNT=1;FS=16.698;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=35.36;MQ0=519;MQRankSum=4.516;NLOD=40.59;ReadPosRankSum=-4.992;TLOD=5.23;ANN=T|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000437865|retained_intron||n.*2058G>A|||||2058|,T|downstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000422716|lincRNA||n.*3667G>A|||||3667|,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000438000|lincRNA|1/3|n.60-11064C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000447407|lincRNA|1/3|n.60-11064C>T||||||,T|intron_variant|MODIFIER|RP11-782C8.1|ENSG00000230850|transcript|ENST00000428930|lincRNA|1/2|n.60-21709C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-782C8.2|ENSG00000232274|transcript|ENST00000412204|lincRNA|1/9|n.1501G>A|||||| GT:AD:AF:DP 0/1:513,8:0.023:521 0/0:397,43:0.124:440 | |
| chr1 143239181 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=278;ECNT=3;FS=9.202;HCNT=8;MAX_ED=20;MIN_ED=8;MQ=47.73;MQ0=45;MQRankSum=-2.554;NLOD=9.65;ReadPosRankSum=-3.073;TLOD=8.34;ANN=C|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000412196|lincRNA||n.-1466A>G|||||1466|,C|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000449527|lincRNA||n.-1466A>G|||||1466|,C|downstream_gene_variant|MODIFIER|RP11-782C8.6|ENSG00000231289|transcript|ENST00000411717|processed_pseudogene||n.*4628A>G|||||4628|,C|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000422716|lincRNA|1/8|n.151+1108A>G||||||,C|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000429121|lincRNA|1/7|n.141+1108A>G||||||,C|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000453561|lincRNA|1/1|n.126+1108A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:143,6:0.038:149:0|1:143239181_T_C 0/0:74,1:0.019:75:0|1:143239181_T_C | |
| chr1 143239189 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=289;ECNT=3;FS=11.882;HCNT=8;MAX_ED=20;MIN_ED=8;MQ=47.79;MQ0=50;MQRankSum=-1.604;NLOD=10.85;ReadPosRankSum=-1.898;TLOD=4.68;ANN=T|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000412196|lincRNA||n.-1474G>A|||||1474|,T|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000449527|lincRNA||n.-1474G>A|||||1474|,T|downstream_gene_variant|MODIFIER|RP11-782C8.6|ENSG00000231289|transcript|ENST00000411717|processed_pseudogene||n.*4620G>A|||||4620|,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000422716|lincRNA|1/8|n.151+1100G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000429121|lincRNA|1/7|n.141+1100G>A||||||,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000453561|lincRNA|1/1|n.126+1100G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:147,2:0.019:149:0|1:143239181_T_C 0/0:80,1:0.017:81:0|1:143239181_T_C | |
| chr1 143239201 . A T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=294;ECNT=3;FS=11.609;HCNT=8;MAX_ED=20;MIN_ED=8;MQ=48.31;MQ0=50;MQRankSum=-1.667;NLOD=10.85;ReadPosRankSum=-2.864;TLOD=4.67;ANN=T|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000412196|lincRNA||n.-1486T>A|||||1486|,T|upstream_gene_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000449527|lincRNA||n.-1486T>A|||||1486|,T|downstream_gene_variant|MODIFIER|RP11-782C8.6|ENSG00000231289|transcript|ENST00000411717|processed_pseudogene||n.*4608T>A|||||4608|,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000422716|lincRNA|1/8|n.151+1088T>A||||||,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000429121|lincRNA|1/7|n.141+1088T>A||||||,T|intron_variant|MODIFIER|RP11-782C8.5|ENSG00000225278|transcript|ENST00000453561|lincRNA|1/1|n.126+1088T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:150,2:0.018:152:0|1:143239181_T_C 0/0:82,1:0.017:83:0|1:143239181_T_C | |
| chr1 143364877 . G T . PASS ClippingRankSum=0;DP=1814;ECNT=1;FS=15.115;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=31.06;MQ0=1157;MQRankSum=1.418;NLOD=3.51;ReadPosRankSum=0.746;TLOD=11.30;ANN=T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA|7/11|n.585G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000424820|lincRNA|6/7|n.440G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA|4/8|n.215G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA|2/6|n.380G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000446530|lincRNA|2/5|n.114G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000411775|lincRNA|3/6|n.153G>T||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.3|ENSG00000242569|transcript|ENST00000442663|lincRNA|2/4|n.97G>T||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|2/3|n.147+2779C>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-7772C>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|3/4|n.603+2779C>A|||||| GT:AD:AF:DP 0/1:175,9:0.05:184 0/0:407,40:0.099:447 | |
| chr1 143380441 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1186;ECNT=9;FS=15.465;HCNT=9;MAX_ED=200;MIN_ED=62;MQ=30.34;MQ0=816;MQRankSum=-2.734;NLOD=13.03;ReadPosRankSum=-4.302;TLOD=9.56;ANN=T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3742C>T|||||3742|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3612C>T|||||3612|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3704C>T|||||3704|,T|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1804G>A|||||1804|,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12698G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|1/5|n.1634-23C>T||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23336G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12698G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|1/1|n.179-23C>T|||||| GT:AD:AF:DP 0/1:65,7:0.097:72 0/0:278,10:0.046:288 | |
| chr1 143380503 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1529;ECNT=9;FS=2.196;HCNT=32;MAX_ED=200;MIN_ED=62;MQ=30.84;MQ0=928;MQRankSum=-3.062;NLOD=10.19;ReadPosRankSum=0.531;TLOD=44.82;ANN=T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3804C>T|||||3804|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3674C>T|||||3674|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3766C>T|||||3766|,T|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1742G>A|||||1742|,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12760G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23398G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12760G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/6|n.1673C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.218C>T|||||| GT:AD:AF:DP 0/1:180,29:0.139:209 0/0:333,35:0.096:368 | |
| chr1 143380533 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1614;ECNT=9;FS=3.035;HCNT=17;MAX_ED=200;MIN_ED=62;MQ=31.61;MQ0=892;MQRankSum=4.619;NLOD=5.75;ReadPosRankSum=2.504;TLOD=4.01;ANN=T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3834C>T|||||3834|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3704C>T|||||3704|,T|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3796C>T|||||3796|,T|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1712G>A|||||1712|,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12790G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23428G>A||||||,T|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12790G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/6|n.1703C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.248C>T|||||| GT:AD:AF:DP 0/1:290,5:0.017:295 0/0:354,44:0.093:398 | |
| chr1 143380579 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1730;ECNT=9;FS=1.777;HCNT=27;MAX_ED=200;MIN_ED=62;MQ=33.51;MQ0=668;MQRankSum=-4.871;NLOD=1.68;ReadPosRankSum=1.375;TLOD=128.34;ANN=C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3880T>C|||||3880|,C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3750T>C|||||3750|,C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3842T>C|||||3842|,C|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1666A>G|||||1666|,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12836A>G||||||,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23474A>G||||||,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12836A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/6|n.1749T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.294T>C|||||| GT:AD:AF:DP 0/1:466,76:0.115:542 0/0:394,47:0.106:441 | |
| chr1 143380611 . CA C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1623;ECNT=9;FS=3.263;HCNT=18;MAX_ED=200;MIN_ED=62;MQ=34.76;MQ0=480;MQRankSum=-4.011;NLOD=6.48;ReadPosRankSum=1.595;TLOD=128.81;ANN=C|splice_region_variant&non_coding_transcript_exon_variant|LOW|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/6|n.1783delA||||||INFO_REALIGN_3_PRIME,C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3913delA|||||3913|,C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3783delA|||||3783|,C|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3875delA|||||3875|,C|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1633delT|||||1633|,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12869delT||||||,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23507delT||||||,C|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12869delT||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.328delA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:571,66:0.098:637:0|1:143380611_CA_C 0/0:367,40:0.102:407:0|1:143380611_CA_C | |
| chr1 143380625 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1565;ECNT=9;FS=3.406;HCNT=18;MAX_ED=200;MIN_ED=62;MQ=35.42;MQ0=401;MQRankSum=-3.892;NLOD=9.80;ReadPosRankSum=-0.713;TLOD=130.76;ANN=G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3926A>G|||||3926|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3796A>G|||||3796|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3888A>G|||||3888|,G|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1620T>C|||||1620|,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12882T>C||||||,G|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/5|n.1783+12A>G||||||,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23520T>C||||||,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12882T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.340A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:621,63:0.09:684:0|1:143380611_CA_C 0/0:362,37:0.096:399:0|1:143380611_CA_C | |
| chr1 143380630 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1543;ECNT=9;FS=3.65;HCNT=18;MAX_ED=200;MIN_ED=62;MQ=35.7;MQ0=380;MQRankSum=-3.97;NLOD=11.00;ReadPosRankSum=-1.854;TLOD=133.85;ANN=A|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3931G>A|||||3931|,A|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3801G>A|||||3801|,A|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3893G>A|||||3893|,A|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1615C>T|||||1615|,A|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12887C>T||||||,A|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/5|n.1783+17G>A||||||,A|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23525C>T||||||,A|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12887C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.345G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:626,60:0.09:686:0|1:143380611_CA_C 0/0:362,34:0.09:396:0|1:143380611_CA_C | |
| chr1 143380640 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1514;ECNT=9;FS=8.512;HCNT=7;MAX_ED=200;MIN_ED=62;MQ=36.13;MQ0=343;MQRankSum=4;NLOD=15.50;ReadPosRankSum=1.664;TLOD=10.38;ANN=G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3941T>G|||||3941|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3811T>G|||||3811|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3903T>G|||||3903|,G|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1605A>C|||||1605|,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12897A>C||||||,G|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/5|n.1783+27T>G||||||,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23535A>C||||||,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12897A>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.355T>G|||||| GT:AD:AF:DP 0/1:698,5:0.01:703 0/0:363,22:0.059:385 | |
| chr1 143380641 . GT G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1513;ECNT=9;FS=3.957;HCNT=18;MAX_ED=200;MIN_ED=62;MQ=36.2;MQ0=339;MQRankSum=-4.946;NLOD=8.23;ReadPosRankSum=-4.92;TLOD=135.13;ANN=G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000430699|lincRNA||n.*3943delT|||||3943|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000431621|lincRNA||n.*3813delT|||||3813|,G|downstream_gene_variant|MODIFIER|RP11-435B5.3|ENSG00000242569|transcript|ENST00000444754|lincRNA||n.*3905delT|||||3905|,G|downstream_gene_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000432361|lincRNA||n.*1603delA|||||1603|,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000423249|lincRNA|1/3|n.60-12899delA||||||,G|intron_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000428624|lincRNA|2/5|n.1783+30delT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000443548|lincRNA|2/3|n.127-23537delA||||||,G|intron_variant|MODIFIER|RP11-435B5.4|ENSG00000185044|transcript|ENST00000424068|lincRNA|2/4|n.516-12899delA||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-435B5.5|ENSG00000238261|transcript|ENST00000423394|lincRNA|2/2|n.358delT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:649,59:0.091:708:0|1:143380611_CA_C 0/0:357,27:0.083:384:0|1:143380611_CA_C | |
| chr1 143744418 . C T . PASS ClippingRankSum=0;DP=646;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=45.25;MQ0=136;MQRankSum=0.133;NLOD=34.42;ReadPosRankSum=-5.625;TLOD=10.58;ANN=T|upstream_gene_variant|MODIFIER|RP6-206I17.1|ENSG00000223804|transcript|ENST00000445753|lincRNA||n.-8G>A|||||8|,T|upstream_gene_variant|MODIFIER|RP6-206I17.1|ENSG00000223804|transcript|ENST00000418192|lincRNA||n.-63G>A|||||63|,T|intron_variant|MODIFIER|RP6-206I17.1|ENSG00000223804|transcript|ENST00000440862|lincRNA|1/1|n.207+93G>A||||||,T|intron_variant|MODIFIER|RP6-206I17.1|ENSG00000223804|transcript|ENST00000429388|lincRNA|1/1|n.88-120G>A|||||| GT:AD:AF:DP 0/1:209,7:0.036:216 0/0:236,13:0.06:249 | |
| chr1 144621611 . C G . PASS ClippingRankSum=0;DP=977;ECNT=1;FS=8.657;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=51.79;MQ0=88;MQRankSum=-2.57;NLOD=28.93;ReadPosRankSum=1.363;TLOD=11.05;ANN=G|downstream_gene_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000449960|processed_transcript||n.*1572C>G|||||1572|,G|downstream_gene_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000423405|processed_transcript||n.*1517C>G|||||1517|,G|downstream_gene_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000437133|processed_transcript||n.*1517C>G|||||1517|,G|downstream_gene_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000448172|processed_transcript||n.*2192C>G|||||2192|,G|downstream_gene_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000427261|processed_transcript||n.*63C>G|||||63|,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000429694|processed_transcript|11/11|n.2243C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000421407|processed_transcript|12/12|n.2083C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000446541|processed_transcript|9/9|n.1385C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000428366|processed_transcript|6/6|n.1484C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000334866|transcribed_unprocessed_pseudogene|5/5|n.838C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-640M9.2|ENSG00000225241|transcript|ENST00000589820|transcribed_unprocessed_pseudogene|6/6|n.941C>G|||||| GT:AD:AF:DP 0/1:535,8:0.022:543 0/0:280,12:0.052:292 | |
| chr1 144676632 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=595;ECNT=2;FS=3.818;HCNT=14;MAX_ED=14;MIN_ED=14;MQ=55.53;MQ0=18;MQRankSum=-5.004;NLOD=29.00;ReadPosRankSum=1.233;TLOD=7.39;ANN=C|downstream_gene_variant|MODIFIER|WI2-1896O14.1|ENSG00000215861|transcript|ENST00000313342|unprocessed_pseudogene||n.*242A>G|||||242|,C|intergenic_region|MODIFIER|RP11-640M9.2-WI2-1896O14.1|ENSG00000225241-ENSG00000215861|intergenic_region|ENSG00000225241-ENSG00000215861|||n.144676632T>C|||||| GT:AD:AF:DP 0/1:387,14:0.024:401 0/0:166,6:0.023:172 | |
| chr1 144676646 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=661;ECNT=2;FS=8.86;HCNT=29;MAX_ED=14;MIN_ED=14;MQ=56.24;MQ0=18;MQRankSum=-8.068;NLOD=12.20;ReadPosRankSum=-0.393;TLOD=38.73;ANN=C|downstream_gene_variant|MODIFIER|WI2-1896O14.1|ENSG00000215861|transcript|ENST00000313342|unprocessed_pseudogene||n.*228A>G|||||228|,C|intergenic_region|MODIFIER|RP11-640M9.2-WI2-1896O14.1|ENSG00000225241-ENSG00000215861|intergenic_region|ENSG00000225241-ENSG00000215861|||n.144676646T>C|||||| GT:AD:AF:DP 0/1:410,30:0.061:440 0/0:188,11:0.062:199 | |
| chr1 144813824 . G C . PASS ClippingRankSum=0;DP=362;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=47.75;MQ0=24;MQRankSum=-1.882;NLOD=5.02;ReadPosRankSum=3.957;TLOD=13.81;ANN=C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|2/15|c.291G>C|p.Leu97Leu|293/3680|291/2049|97/682||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|2/14|c.297G>C|p.Leu99Leu|297/3347|297/1830|99/609||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|2/16|c.297G>C|p.Leu99Leu|297/3568|297/1824|99/607||WARNING_TRANSCRIPT_NO_START_CODON,C|5_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|2/13|c.-649G>C|||||8179|,C|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000465793|processed_transcript||n.-736G>C|||||736|,C|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000471873|processed_transcript||n.-859G>C|||||859|,C|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000484811|processed_transcript||n.-1987G>C|||||1987|,C|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript||n.-2120G>C|||||2120|,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000483630|processed_transcript|2/4|n.293G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|2/15|n.293G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|2/13|n.293G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|2/15|n.293G>C|||||| GT:AD:AF:DP 0/1:181,12:0.059:193 0/0:105,9:0.092:114 | |
| chr1 144816651 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=950;ECNT=2;FS=14.327;HCNT=6;MAX_ED=5;MIN_ED=5;MQ=58.34;MQ0=24;MQRankSum=-7.352;NLOD=21.32;ReadPosRankSum=-6.641;TLOD=13.92;ANN=T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|5/15|c.778C>T|p.Arg260Trp|780/3680|778/2049|260/682||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|5/14|c.784C>T|p.Arg262Trp|784/3347|784/1830|262/609||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|5/16|c.784C>T|p.Arg262Trp|784/3568|784/1824|262/607||WARNING_TRANSCRIPT_NO_START_CODON,T|5_prime_UTR_premature_start_codon_gain_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|5/13|c.-162C>T||||||,T|5_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|5/13|c.-162C>T|||||5352|,T|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.-4325C>T|||||4325|,T|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000483630|processed_transcript||n.*1390C>T|||||1390|,T|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000465793|processed_transcript||n.*602C>T|||||602|,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|5/15|n.780C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|5/13|n.780C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|5/15|n.780C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000471873|processed_transcript|3/3|n.621C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000484811|processed_transcript|2/2|n.377C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript|2/3|n.244C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:615,11:0.026:626:0|1:144816651_C_T 0/0:266,22:0.101:288:0|1:144816651_C_T | |
| chr1 144816656 . A C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=879;ECNT=2;FS=2.933;HCNT=6;MAX_ED=5;MIN_ED=5;MQ=58.52;MQ0=22;MQRankSum=-0.921;NLOD=30.90;ReadPosRankSum=-1.574;TLOD=5.97;ANN=C|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|5/15|c.783A>C|p.Glu261Asp|785/3680|783/2049|261/682||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|5/14|c.789A>C|p.Glu263Asp|789/3347|789/1830|263/609||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|5/16|c.789A>C|p.Glu263Asp|789/3568|789/1824|263/607||WARNING_TRANSCRIPT_NO_START_CODON,C|5_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|5/13|c.-157A>C|||||5347|,C|upstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.-4320A>C|||||4320|,C|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000483630|processed_transcript||n.*1395A>C|||||1395|,C|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000465793|processed_transcript||n.*607A>C|||||607|,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|5/15|n.785A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|5/13|n.785A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|5/15|n.785A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000471873|processed_transcript|3/3|n.626A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000484811|processed_transcript|2/2|n.382A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript|2/3|n.249A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:592,1:0.014:593:0|1:144816651_C_T 0/0:244,10:0.085:254:0|1:144816651_C_T | |
| chr1 144823135 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2290;ECNT=4;FS=6.622;HCNT=3;MAX_ED=46;MIN_ED=41;MQ=39.45;MQ0=706;MQRankSum=-0.058;NLOD=66.09;ReadPosRankSum=-5.625;TLOD=15.71;ANN=C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|8/15|c.1029G>C|p.Arg343Arg|1031/3680|1029/2049|343/682||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|8/14|c.1035G>C|p.Arg345Arg|1035/3347|1035/1830|345/609||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|8/16|c.1035G>C|p.Arg345Arg|1035/3568|1035/1824|345/607||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|8/13|c.90G>C|p.Arg30Arg|836/2886|90/624|30/207||,C|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript||n.*4825G>C|||||4825|,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|8/15|n.1107G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|8/13|n.995G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|8/15|n.951G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript|1/6|n.2160G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|1/8|n.574G>C|||||| GT:AD:AF:DP 0/1:850,21:0.037:871 0/0:643,31:0.051:674 | |
| chr1 144823176 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2719;ECNT=4;FS=8.012;HCNT=4;MAX_ED=46;MIN_ED=41;MQ=36.37;MQ0=1173;MQRankSum=0.29;NLOD=24.31;ReadPosRankSum=-0.528;TLOD=28.73;ANN=A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|8/15|c.1070C>A|p.Pro357His|1072/3680|1070/2049|357/682||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|8/14|c.1076C>A|p.Pro359His|1076/3347|1076/1830|359/609||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|8/16|c.1076C>A|p.Pro359His|1076/3568|1076/1824|359/607||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|8/13|c.131C>A|p.Pro44His|877/2886|131/624|44/207||,A|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript||n.*4866C>A|||||4866|,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|8/15|n.1148C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|8/13|n.1036C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|8/15|n.992C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript|1/6|n.2201C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|1/8|n.615C>A|||||| GT:AD:AF:DP 0/1:681,27:0.052:708 0/0:720,45:0.069:765 | |
| chr1 144823177 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2733;ECNT=4;FS=3.669;HCNT=2;MAX_ED=46;MIN_ED=41;MQ=36.3;MQ0=1188;MQRankSum=2.325;NLOD=71.39;ReadPosRankSum=-0.719;TLOD=26.29;ANN=G|splice_region_variant&synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|8/15|c.1071C>G|p.Pro357Pro|1073/3680|1071/2049|357/682||WARNING_TRANSCRIPT_NO_START_CODON,G|splice_region_variant&synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|8/14|c.1077C>G|p.Pro359Pro|1077/3347|1077/1830|359/609||WARNING_TRANSCRIPT_NO_START_CODON,G|splice_region_variant&synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|8/16|c.1077C>G|p.Pro359Pro|1077/3568|1077/1824|359/607||WARNING_TRANSCRIPT_NO_START_CODON,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|8/15|n.1149C>G||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|8/13|n.1037C>G||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|8/15|n.993C>G||||||,G|splice_region_variant&synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|8/13|c.132C>G|p.Pro44Pro|878/2886|132/624|44/207||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript|1/6|n.2202C>G||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|1/8|n.616C>G||||||,G|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript||n.*4867C>G|||||4867| GT:AD:AF:DP:PGT:PID 0/1:700,11:0.021:711:0|1:144823177_C_G 0/0:739,41:0.049:780:0|1:144823177_C_G | |
| chr1 144823181 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2751;ECNT=4;FS=3.669;HCNT=2;MAX_ED=46;MIN_ED=41;MQ=35.98;MQ0=1225;MQRankSum=2.274;NLOD=69.59;ReadPosRankSum=0.351;TLOD=26.30;ANN=C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|8/14|c.1073+2T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|8/13|c.1079+2T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|8/15|c.1079+2T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|8/14|n.1151+2T>C||||||,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|8/12|n.1039+2T>C||||||,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|8/14|n.995+2T>C||||||,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|8/12|c.134+2T>C||||||,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript|1/5|n.2204+2T>C||||||,C|splice_donor_variant&intron_variant|HIGH|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|1/7|n.618+2T>C||||||,C|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000472811|processed_transcript||n.*4871T>C|||||4871|;LOF=(NBPF9|ENSG00000168614|14|0.29) GT:AD:AF:DP:PGT:PID 0/1:682,11:0.021:693:0|1:144823177_C_G 0/0:736,41:0.05:777:0|1:144823177_C_G | |
| chr1 144828583 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=323;ECNT=7;FS=29.949;HCNT=6;MAX_ED=124;MIN_ED=16;MQ=52.07;MQ0=3;MQRankSum=0.094;NLOD=9.18;ReadPosRankSum=-1.233;TLOD=7.64;ANN=A|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1848G>A|p.Leu616Leu|1850/3680|1848/2049|616/682||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1629G>A|p.Leu543Leu|1629/3347|1629/1830|543/609||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.423G>A|p.Leu141Leu|1169/2886|423/624|141/207||,A|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*26G>A|||||26|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4585C>T|||||4585|,A|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*718G>A|||||718|,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.1926G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1532G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1770G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1393G>A|||||| GT:AD:AF:DP 0/1:207,4:0.026:211 0/0:95,7:0.092:102 | |
| chr1 144828599 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=369;ECNT=7;FS=6.74;HCNT=3;MAX_ED=124;MIN_ED=16;MQ=50.1;MQ0=12;MQRankSum=1.828;NLOD=10.90;ReadPosRankSum=-0.373;TLOD=4.27;ANN=A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1864G>A|p.Gly622Arg|1866/3680|1864/2049|622/682||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1645G>A|p.Gly549Arg|1645/3347|1645/1830|549/609||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.439G>A|p.Gly147Arg|1185/2886|439/624|147/207||,A|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*42G>A|||||42|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4569C>T|||||4569|,A|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*734G>A|||||734|,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.1942G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1548G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1786G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1409G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:232,2:0.012:234:0|1:144828599_G_A 0/0:106,9:0.111:115:0|1:144828599_G_A | |
| chr1 144828610 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=385;ECNT=7;FS=4.278;HCNT=6;MAX_ED=124;MIN_ED=16;MQ=49.14;MQ0=15;MQRankSum=1.362;NLOD=10.27;ReadPosRankSum=-0.111;TLOD=8.19;ANN=G|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1875T>G|p.Ser625Ser|1877/3680|1875/2049|625/682||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1656T>G|p.Ser552Ser|1656/3347|1656/1830|552/609||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.450T>G|p.Ser150Ser|1196/2886|450/624|150/207||,G|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*53T>G|||||53|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4558A>C|||||4558|,G|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*745T>G|||||745|,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.1953T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1559T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1797T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1420T>G|||||| GT:AD:AF:DP 0/1:240,3:0.022:243 0/0:110,9:0.128:119 | |
| chr1 144828618 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=426;ECNT=7;FS=0.945;HCNT=3;MAX_ED=124;MIN_ED=16;MQ=47.53;MQ0=26;MQRankSum=1.902;NLOD=13.61;ReadPosRankSum=-1.071;TLOD=6.54;ANN=T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1883C>T|p.Ser628Leu|1885/3680|1883/2049|628/682||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1664C>T|p.Ser555Leu|1664/3347|1664/1830|555/609||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.458C>T|p.Ser153Leu|1204/2886|458/624|153/207||,T|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*61C>T|||||61|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4550G>A|||||4550|,T|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*753C>T|||||753|,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.1961C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1567C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1805C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1428C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:251,4:0.021:255:0|1:144828599_G_A 0/0:118,13:0.117:131:0|1:144828599_G_A | |
| chr1 144828683 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=658;ECNT=7;FS=6.066;HCNT=4;MAX_ED=124;MIN_ED=16;MQ=48.53;MQ0=70;MQRankSum=-2.342;NLOD=20.23;ReadPosRankSum=-2.834;TLOD=17.48;ANN=G|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1948C>G|p.Gln650Glu|1950/3680|1948/2049|650/682||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1729C>G|p.Gln577Glu|1729/3347|1729/1830|577/609||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.523C>G|p.Gln175Glu|1269/2886|523/624|175/207||,G|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*126C>G|||||126|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4485G>C|||||4485|,G|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*818C>G|||||818|,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.2026C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1632C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1870C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1493C>G|||||| GT:AD:AF:DP:PGT:PID 0/1:363,7:0.027:370:0|1:144828683_C_G 0/0:199,4:0.026:203:0|1:144828683_C_G | |
| chr1 144828688 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=671;ECNT=7;FS=9.14;HCNT=4;MAX_ED=124;MIN_ED=16;MQ=48.84;MQ0=72;MQRankSum=-2.326;NLOD=16.03;ReadPosRankSum=-2.97;TLOD=24.37;ANN=T|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1953C>T|p.His651His|1955/3680|1953/2049|651/682||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1734C>T|p.His578His|1734/3347|1734/1830|578/609||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.528C>T|p.His176His|1274/2886|528/624|176/207||,T|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*131C>T|||||131|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4480G>A|||||4480|,T|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*823C>T|||||823|,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.2031C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1637C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1875C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1498C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:363,8:0.037:371:0|1:144828683_C_G 0/0:208,5:0.032:213:0|1:144828683_C_G | |
| chr1 144828707 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=710;ECNT=7;FS=21.251;HCNT=4;MAX_ED=124;MIN_ED=16;MQ=50.1;MQ0=72;MQRankSum=-3.303;NLOD=6.33;ReadPosRankSum=-4.509;TLOD=38.68;ANN=T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000375552|protein_coding|15/15|c.1972G>T|p.Val658Leu|1974/3680|1972/2049|658/682||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000338347|protein_coding|14/14|c.1753G>T|p.Val585Leu|1753/3347|1753/1830|585/609||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF9|ENSG00000168614|transcript|ENST00000281815|protein_coding|13/13|c.547G>T|p.Val183Leu|1293/2886|547/624|183/207||,T|3_prime_UTR_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000440491|protein_coding|16/16|c.*150G>T|||||150|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|RP4-791M13.3|ENSG00000254539|transcript|ENST00000466343|antisense||n.*4461C>A|||||4461|,T|downstream_gene_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000488888|processed_transcript||n.*842G>T|||||842|,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000468645|processed_transcript|15/15|n.2050G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000491652|processed_transcript|13/13|n.1656G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000496755|processed_transcript|15/15|n.1894G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|NBPF9|ENSG00000168614|transcript|ENST00000473761|processed_transcript|8/8|n.1517G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:379,18:0.065:397:0|1:144828683_C_G 0/0:215,11:0.055:226:0|1:144828683_C_G | |
| chr1 144852508 . AAACAT A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=896;ECNT=3;FS=2.033;HCNT=10;MAX_ED=14;MIN_ED=10;MQ=56.62;MQ0=2;MQRankSum=1.899;NLOD=12.78;ReadPosRankSum=-0.533;TLOD=18.90;ANN=A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533768|retained_intron||n.*1854_*1858delATGTT|||||1858|,A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000534367|retained_intron||n.*3258_*3262delATGTT|||||3262|,A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530130|protein_coding||c.*3343_*3347delATGTT|||||3347|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526664|processed_transcript||n.*4486_*4490delATGTT|||||4490|,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|46/46|c.7408-14_7408-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000531417|processed_transcript|2/4|n.102-14_102-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525630|processed_transcript|4/6|n.400-14_400-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000460027|processed_transcript|1/2|n.34-14_34-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|45/45|c.6682-14_6682-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|25/25|n.4434-14_4434-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|43/43|c.7000-14_7000-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|43/43|c.7000-70_7000-66delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|45/45|c.7255-14_7255-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000464924|retained_intron|1/1|n.287-14_287-10delATGTT||||||,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|5/5|c.*456-14_*456-10delATGTT||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526182|processed_transcript|1/1|n.77-14_77-10delATGTT||||||,A|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524688|retained_intron|1/2|n.413_417delATGTT|||||| GT:AD:AF:DP:PGT:PID 0/1:576,9:0.02:585:0|1:144852508_AAACAT_A 0/0:260,12:0.052:272:0|1:144852508_AAACAT_A | |
| chr1 144852518 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=844;ECNT=3;FS=2.008;HCNT=10;MAX_ED=14;MIN_ED=10;MQ=56.54;MQ0=2;MQRankSum=2.038;NLOD=6.79;ReadPosRankSum=-1.732;TLOD=19.07;ANN=T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533768|retained_intron||n.*1849G>A|||||1849|,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000534367|retained_intron||n.*3253G>A|||||3253|,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530130|protein_coding||c.*3338G>A|||||3338|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526664|processed_transcript||n.*4481G>A|||||4481|,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|46/46|c.7408-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000531417|processed_transcript|2/4|n.102-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525630|processed_transcript|4/6|n.400-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000460027|processed_transcript|1/2|n.34-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|45/45|c.6682-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|25/25|n.4434-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|43/43|c.7000-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|43/43|c.7000-75G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|45/45|c.7255-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000464924|retained_intron|1/1|n.287-19G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|5/5|c.*456-19G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526182|processed_transcript|1/1|n.77-19G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524688|retained_intron|1/2|n.408G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:548,9:0.021:557:0|1:144852508_AAACAT_A 0/0:257,13:0.058:270:0|1:144852508_AAACAT_A | |
| chr1 144852522 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=838;ECNT=3;FS=1.991;HCNT=10;MAX_ED=14;MIN_ED=10;MQ=56.56;MQ0=2;MQRankSum=2.04;NLOD=1.99;ReadPosRankSum=-1.605;TLOD=21.99;ANN=T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533768|retained_intron||n.*1845G>A|||||1845|,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000534367|retained_intron||n.*3249G>A|||||3249|,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530130|protein_coding||c.*3334G>A|||||3334|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526664|processed_transcript||n.*4477G>A|||||4477|,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|46/46|c.7408-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000531417|processed_transcript|2/4|n.102-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525630|processed_transcript|4/6|n.400-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000460027|processed_transcript|1/2|n.34-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|45/45|c.6682-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|25/25|n.4434-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|43/43|c.7000-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|43/43|c.7000-79G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|45/45|c.7255-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000464924|retained_intron|1/1|n.287-23G>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|5/5|c.*456-23G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526182|processed_transcript|1/1|n.77-23G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524688|retained_intron|1/2|n.404G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:543,9:0.024:552:0|1:144852508_AAACAT_A 0/0:257,13:0.064:270:0|1:144852508_AAACAT_A | |
| chr1 144879484 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=357;ECNT=7;FS=12.921;HCNT=4;MAX_ED=58;MIN_ED=4;MQ=59.85;MQ0=0;MQRankSum=-6.567;NLOD=12.99;ReadPosRankSum=-1.884;TLOD=4.29;ANN=C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4374A>G|p.Thr1458Thr|4413/8458|4374/7449|1458/2482||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3834A>G|p.Thr1278Thr|4227/8150|3834/6723|1278/2240||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3966A>G|p.Thr1322Thr|4156/8262|3966/7041|1322/2346||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3966A>G|p.Thr1322Thr|4257/8307|3966/7089|1322/2362||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4374A>G|p.Thr1458Thr|4413/8305|4374/7296|1458/2431||,C|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3461A>G|||||3461|,C|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1321T>C|||||1321|,C|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2089T>C|||||2089|,C|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1317A>G|||||1317|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21756A>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15160A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1400A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:230,1:0.012:231:0|1:144879484_T_C 0/0:122,3:0.034:125:0|1:144879484_T_C | |
| chr1 144879488 . G C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=357;ECNT=7;FS=16.445;HCNT=4;MAX_ED=58;MIN_ED=4;MQ=59.8;MQ0=0;MQRankSum=-9.647;NLOD=13.59;ReadPosRankSum=-2.065;TLOD=4.25;ANN=C|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4370C>G|p.Ser1457*|4409/8458|4370/7449|1457/2482||,C|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3830C>G|p.Ser1277*|4223/8150|3830/6723|1277/2240||,C|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3962C>G|p.Ser1321*|4152/8262|3962/7041|1321/2346||,C|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3962C>G|p.Ser1321*|4253/8307|3962/7089|1321/2362||,C|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4370C>G|p.Ser1457*|4409/8305|4370/7296|1457/2431||,C|sequence_feature|MODERATE|PDE4DIP|ENSG00000178104|modified-residue:phosphoserine|ENST00000369354|protein_coding|27/44|c.3962C>G||||||,C|sequence_feature|MODERATE|PDE4DIP|ENSG00000178104|modified-residue:phosphoserine|ENST00000369356|protein_coding|27/44|c.3962C>G||||||,C|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3465C>G|||||3465|,C|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1325G>C|||||1325|,C|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2093G>C|||||2093|,C|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1313C>G|||||1313|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21760C>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15164C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1396C>G||||||;LOF=(PDE4DIP|ENSG00000178104|63|0.08);NMD=(PDE4DIP|ENSG00000178104|63|0.08) GT:AD:AF:DP:PGT:PID 0/1:231,2:0.011:233:0|1:144879484_T_C 0/0:120,3:0.033:123:0|1:144879484_T_C | |
| chr1 144879498 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=356;ECNT=7;FS=17.669;HCNT=4;MAX_ED=58;MIN_ED=4;MQ=59.38;MQ0=0;MQRankSum=-9.963;NLOD=8.43;ReadPosRankSum=-2.81;TLOD=15.07;ANN=A|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4360C>T|p.Arg1454Cys|4399/8458|4360/7449|1454/2482||,A|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3820C>T|p.Arg1274Cys|4213/8150|3820/6723|1274/2240||,A|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3952C>T|p.Arg1318Cys|4142/8262|3952/7041|1318/2346||,A|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3952C>T|p.Arg1318Cys|4243/8307|3952/7089|1318/2362||,A|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4360C>T|p.Arg1454Cys|4399/8305|4360/7296|1454/2431||,A|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3475C>T|||||3475|,A|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1335G>A|||||1335|,A|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2103G>A|||||2103|,A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1303C>T|||||1303|WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21770C>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15174C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1386C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:235,6:0.035:241:0|1:144879484_T_C 0/0:110,3:0.048:113:0|1:144879484_T_C | |
| chr1 144879499 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=355;ECNT=7;FS=23.119;HCNT=4;MAX_ED=58;MIN_ED=4;MQ=59.35;MQ0=0;MQRankSum=-10.14;NLOD=8.73;ReadPosRankSum=-3.523;TLOD=15.05;ANN=C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4359A>G|p.Gly1453Gly|4398/8458|4359/7449|1453/2482||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3819A>G|p.Gly1273Gly|4212/8150|3819/6723|1273/2240||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3951A>G|p.Gly1317Gly|4141/8262|3951/7041|1317/2346||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3951A>G|p.Gly1317Gly|4242/8307|3951/7089|1317/2362||,C|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4359A>G|p.Gly1453Gly|4398/8305|4359/7296|1453/2431||,C|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3476A>G|||||3476|,C|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1336T>C|||||1336|,C|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2104T>C|||||2104|,C|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1302A>G|||||1302|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21771A>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15175A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1385A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:233,7:0.034:240:0|1:144879484_T_C 0/0:109,4:0.046:113:0|1:144879484_T_C | |
| chr1 144879501 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=358;ECNT=7;FS=23.199;HCNT=4;MAX_ED=58;MIN_ED=4;MQ=59.24;MQ0=0;MQRankSum=-9.273;NLOD=7.52;ReadPosRankSum=-3.102;TLOD=15.14;ANN=A|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4357G>T|p.Gly1453*|4396/8458|4357/7449|1453/2482||,A|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3817G>T|p.Gly1273*|4210/8150|3817/6723|1273/2240||,A|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3949G>T|p.Gly1317*|4139/8262|3949/7041|1317/2346||,A|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3949G>T|p.Gly1317*|4240/8307|3949/7089|1317/2362||,A|stop_gained|HIGH|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4357G>T|p.Gly1453*|4396/8305|4357/7296|1453/2431||,A|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3478G>T|||||3478|,A|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1338C>A|||||1338|,A|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2106C>A|||||2106|,A|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1300G>T|||||1300|WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21773G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15177G>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1383G>T||||||;LOF=(PDE4DIP|ENSG00000178104|63|0.08);NMD=(PDE4DIP|ENSG00000178104|63|0.08) GT:AD:AF:DP:PGT:PID 0/1:234,7:0.035:241:0|1:144879484_T_C 0/0:111,4:0.048:115:0|1:144879484_T_C | |
| chr1 144879538 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=365;ECNT=7;FS=8.196;HCNT=31;MAX_ED=58;MIN_ED=4;MQ=57.56;MQ0=2;MQRankSum=-6.887;NLOD=1.58;ReadPosRankSum=-0.767;TLOD=38.50;ANN=T|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4320G>A|p.Lys1440Lys|4359/8458|4320/7449|1440/2482||,T|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3780G>A|p.Lys1260Lys|4173/8150|3780/6723|1260/2240||,T|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3912G>A|p.Lys1304Lys|4102/8262|3912/7041|1304/2346||,T|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3912G>A|p.Lys1304Lys|4203/8307|3912/7089|1304/2362||,T|synonymous_variant|LOW|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4320G>A|p.Lys1440Lys|4359/8305|4320/7296|1440/2431||,T|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3515G>A|||||3515|,T|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1375C>T|||||1375|,T|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2143C>T|||||2143|,T|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1263G>A|||||1263|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21810G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15214G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1346G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:225,19:0.078:244:0|1:144879538_C_T 0/0:105,6:0.061:111:0|1:144879538_C_T | |
| chr1 144879542 . A G . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=359;ECNT=7;FS=6.619;HCNT=31;MAX_ED=58;MIN_ED=4;MQ=57.47;MQ0=2;MQRankSum=-7.436;NLOD=1.87;ReadPosRankSum=-0.539;TLOD=38.46;ANN=G|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|30/47|c.4316T>C|p.Leu1439Pro|4355/8458|4316/7449|1439/2482||,G|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|30/46|c.3776T>C|p.Leu1259Pro|4169/8150|3776/6723|1259/2240||,G|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369354|protein_coding|27/44|c.3908T>C|p.Leu1303Pro|4098/8262|3908/7041|1303/2346||,G|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000369356|protein_coding|27/44|c.3908T>C|p.Leu1303Pro|4199/8307|3908/7089|1303/2362||,G|missense_variant|MODERATE|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|30/46|c.4316T>C|p.Leu1439Pro|4355/8305|4316/7296|1439/2431||,G|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000479369|retained_intron||n.-3519T>C|||||3519|,G|downstream_gene_variant|MODIFIER|RP4-791M13.5|ENSG00000254913|transcript|ENST00000531288|antisense||n.*1379A>G|||||1379|,G|downstream_gene_variant|MODIFIER|AL138796.1|ENSG00000266739|transcript|ENST00000582173|miRNA||n.*2147A>G|||||2147|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530592|protein_coding||c.*1259T>C|||||1259|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530062|nonsense_mediated_decay|1/5|c.90-21814T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000525886|retained_intron|2/2|n.294-15218T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000524974|processed_transcript|9/26|n.1342T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:218,20:0.081:238:0|1:144879538_C_T 0/0:104,6:0.064:110:0|1:144879538_C_T | |
| chr1 145014784 . C G . germline_risk;t_lod_fstar ClippingRankSum=0;DP=105;ECNT=1;FS=4.217;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.988;ReadPosRankSum=-3.116;TLOD=5.25;ANN=G|upstream_gene_variant|MODIFIER|RP11-326G21.1|ENSG00000272755|transcript|ENST00000610119|antisense||n.-3611C>G|||||3611|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000478649|protein_coding||c.*1055G>C|||||900|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000485062|processed_transcript||n.*1080G>C|||||1080|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530940|processed_transcript||n.*1089G>C|||||1089|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526359|nonsense_mediated_decay||c.*3193G>C|||||1111|,G|downstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000528661|nonsense_mediated_decay||c.*3193G>C|||||1175|,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|3/46|c.441+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|3/45|c.228+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|3/45|c.441+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000532801|protein_coding|3/4|c.195+1109G>C||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000496572|nonsense_mediated_decay|1/3|c.78+1076G>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530078|retained_intron|3/7|n.574+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000497529|processed_transcript|4/5|n.684+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000527063|retained_intron|3/5|n.590+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369348|protein_coding|3/6|c.441+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000532803|processed_transcript|4/7|n.656+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533163|processed_transcript|3/6|n.563+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000528552|processed_transcript|3/6|n.568+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533259|protein_coding|1/3|c.-83+24806G>C||||||WARNING_TRANSCRIPT_NO_STOP_CODON,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530822|nonsense_mediated_decay|3/5|c.228+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000531369|protein_coding|3/5|c.231+1076G>C||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533396|processed_transcript|3/4|n.470+1076G>C||||||,G|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000493130|protein_coding|3/3|c.229-471G>C|||||| GT:AD:AF:DP 0/1:70,3:0.049:73 0/0:28,3:0.074:31 | |
| chr1 145039523 . G T . germline_risk ClippingRankSum=0;DP=149;ECNT=1;FS=1.099;HCNT=38;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.07;ReadPosRankSum=-0.786;TLOD=18.08;ANN=T|upstream_gene_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000531369|protein_coding||c.-584C>A|||||445|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369359|protein_coding|1/46|c.234-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000313382|protein_coding|1/45|c.20+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530740|protein_coding|1/45|c.234-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000532801|protein_coding|1/4|c.20+67C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530078|retained_intron|1/7|n.366+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000497529|processed_transcript|1/5|n.354+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000527063|retained_intron|1/5|n.383-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000369348|protein_coding|1/6|c.234-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000532803|processed_transcript|1/7|n.353+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533163|processed_transcript|1/6|n.355+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000528552|processed_transcript|1/6|n.361-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533259|protein_coding|1/3|c.-83+67C>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530822|nonsense_mediated_decay|1/5|c.20+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000533396|processed_transcript|1/4|n.263-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000493130|protein_coding|1/3|c.20+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000478649|protein_coding|1/2|c.20+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000485062|processed_transcript|1/3|n.276+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000530940|processed_transcript|1/3|n.262+67C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000526359|nonsense_mediated_decay|1/3|c.234-18356C>A||||||,T|intron_variant|MODIFIER|PDE4DIP|ENSG00000178104|transcript|ENST00000528661|nonsense_mediated_decay|1/3|c.234-18356C>A|||||| GT:AD:AF:DP 0/1:92,11:0.117:103 0/0:42,4:0.088:46 | |
| chr1 145109661 . G A . PASS ClippingRankSum=0;DP=489;ECNT=1;FS=0.828;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.30;ReadPosRankSum=0.238;TLOD=66.75;ANN=A|non_coding_transcript_exon_variant|MODIFIER|SEC22B|ENSG00000223380|transcript|ENST00000453618|processed_transcript|3/5|n.650G>A|||||| GT:AD:AF:DP 0/1:284,47:0.142:331 0/0:145,11:0.065:156 | |
| chr1 145209152 . GGGC G . PASS ClippingRankSum=0;DP=541;ECNT=1;FS=9.028;HCNT=21;MAX_ED=.;MIN_ED=.;MQ=50.58;MQ0=5;MQRankSum=-7.118;NLOD=7.79;ReadPosRankSum=-3.849;TLOD=76.33;ANN=G|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000362074|protein_coding|1/5|c.-322_-320delGGC|||||39696|INFO_REALIGN_3_PRIME,G|5_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|1/23|c.-322_-320delGGC|||||39696|INFO_REALIGN_3_PRIME,G|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding|1/6|c.-322_-320delGGC|||||39696|INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:238,35:0.122:273 0/0:163,7:0.051:170 | |
| chr1 145209191 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=390;ECNT=2;FS=16.515;HCNT=13;MAX_ED=132;MIN_ED=132;MQ=52.06;MQ0=1;MQRankSum=-6.173;NLOD=20.40;ReadPosRankSum=-3.898;TLOD=19.86;ANN=C|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000362074|protein_coding|1/5|c.-290G>C|||||39666|,C|5_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|1/23|c.-290G>C|||||39666|,C|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding|1/6|c.-290G>C|||||39666| GT:AD:AF:DP 0/1:189,18:0.098:207 0/0:136,3:0.031:139 | |
| chr1 145209323 . AGGC A . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=121;ECNT=2;FS=1.602;HCNT=14;MAX_ED=132;MIN_ED=132;MQ=54.98;MQ0=8;MQRankSum=-3.778;NLOD=0.762;ReadPosRankSum=-1.613;TLOD=5.49;ANN=A|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000362074|protein_coding|1/5|c.-137_-135delCGG|||||39511|INFO_REALIGN_3_PRIME,A|5_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|1/23|c.-137_-135delCGG|||||39511|INFO_REALIGN_3_PRIME,A|5_prime_UTR_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding|1/6|c.-137_-135delCGG|||||39511|INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:43,4:0.069:47 0/0:29,2:0.056:31 | |
| chr1 145281361 . TC T . germline_risk ClippingRankSum=0;DP=559;ECNT=1;FS=0;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=52.22;MQ0=4;MQRankSum=-0.444;NLOD=1.29;ReadPosRankSum=-1.272;TLOD=41.90;ANN=T|splice_region_variant&intron_variant|LOW|NOTCH2NL|ENSG00000213240|transcript|ENST00000362074|protein_coding|3/4|c.299-6delC||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|3/22|c.299-6delC||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding|3/5|c.299-6delC||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|NOTCH2NL|ENSG00000213240|transcript|ENST00000369340|protein_coding|4/5|c.299-6delC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:355,31:0.077:386 0/0:149,12:0.08:161 | |
| chr1 145293400 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1185;ECNT=4;FS=6.72;HCNT=7;MAX_ED=79;MIN_ED=68;MQ=56.8;MQ0=4;MQRankSum=-5.57;NLOD=41.94;ReadPosRankSum=-4.054;TLOD=20.12;ANN=A|5_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|1/84|c.-6G>A|||||6|,A|5_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/17|c.-6G>A|||||6|,A|5_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|2/19|c.-6G>A|||||6|,A|5_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|2/19|c.-6G>A|||||6|,A|5_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|1/47|c.-6G>A|||||6|,A|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|6/23|c.*102G>A|||||204|,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding||c.*2913G>A|||||1746|,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000479995|processed_transcript||n.*1428G>A|||||1428|,A|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-36+132G>A|||||| GT:AD:AF:DP 0/1:780,21:0.028:801 0/0:338,17:0.054:355 | |
| chr1 145293468 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1603;ECNT=4;FS=3.007;HCNT=5;MAX_ED=79;MIN_ED=68;MQ=58.99;MQ0=5;MQRankSum=-6.557;NLOD=66.98;ReadPosRankSum=-4.005;TLOD=21.00;ANN=T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|1/84|c.63C>T|p.Asn21Asn|98/10697|63/10662|21/3553||,T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/17|c.63C>T|p.Asn21Asn|316/3888|63/2016|21/671||,T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|2/19|c.63C>T|p.Asn21Asn|566/2922|63/192|21/63||,T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|2/19|c.63C>T|p.Asn21Asn|566/2917|63/192|21/63||,T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|1/47|c.63C>T|p.Asn21Asn|98/5348|63/1797|21/598||,T|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|6/23|c.*170C>T|||||272|,T|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding||c.*2981C>T|||||1814|,T|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000479995|processed_transcript||n.*1496C>T|||||1496|,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-36+200C>T|||||| GT:AD:AF:DP 0/1:1079,10:0.013:1089 0/0:492,12:0.029:504 | |
| chr1 145293473 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1641;ECNT=4;FS=3.011;HCNT=6;MAX_ED=79;MIN_ED=68;MQ=58.96;MQ0=5;MQRankSum=-6.739;NLOD=63.84;ReadPosRankSum=-3.285;TLOD=23.43;ANN=A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|1/84|c.68C>A|p.Thr23Lys|103/10697|68/10662|23/3553||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/17|c.68C>A|p.Thr23Lys|321/3888|68/2016|23/671||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|2/19|c.68C>A|p.Thr23Lys|571/2922|68/192|23/63||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|2/19|c.68C>A|p.Thr23Lys|571/2917|68/192|23/63||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|1/47|c.68C>A|p.Thr23Lys|103/5348|68/1797|23/598||,A|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|6/23|c.*175C>A|||||277|,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding||c.*2986C>A|||||1819|,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000479995|processed_transcript||n.*1501C>A|||||1501|,A|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-36+205C>A|||||| GT:AD:AF:DP 0/1:1087,10:0.014:1097 0/0:511,13:0.032:524 | |
| chr1 145293479 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1675;ECNT=4;FS=2.052;HCNT=6;MAX_ED=79;MIN_ED=68;MQ=58.65;MQ0=15;MQRankSum=-8.503;NLOD=61.51;ReadPosRankSum=-4.616;TLOD=20.01;ANN=A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|1/84|c.74G>A|p.Arg25His|109/10697|74/10662|25/3553||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/17|c.74G>A|p.Arg25His|327/3888|74/2016|25/671||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|2/19|c.74G>A|p.Arg25His|577/2922|74/192|25/63||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|2/19|c.74G>A|p.Arg25His|577/2917|74/192|25/63||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|1/47|c.74G>A|p.Arg25His|109/5348|74/1797|25/598||,A|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|6/23|c.*181G>A|||||283|,A|TF_binding_site_variant|MODIFIER|||CTCF|MA0139.1|||n.145293479C>T||||||,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding||c.*2992G>A|||||1825|,A|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000479995|processed_transcript||n.*1507G>A|||||1507|,A|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-36+211G>A|||||| GT:AD:AF:DP 0/1:1094,17:0.016:1111 0/0:516,18:0.036:534 | |
| chr1 145296403 . C T . PASS ClippingRankSum=0;DP=348;ECNT=1;FS=45.953;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=48.34;MQ0=9;MQRankSum=-1.029;NLOD=3.22;ReadPosRankSum=-3.38;TLOD=9.68;ANN=T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|3/84|c.325C>T|p.Leu109Leu|360/10697|325/10662|109/3553||,T|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|3/47|c.325C>T|p.Leu109Leu|360/5348|325/1797|109/598||,T|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|8/23|c.*432C>T|||||3207|,T|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|3/19|c.*30C>T|||||30|,T|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|3/19|c.*30C>T|||||30|,T|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000344859|protein_coding||c.*5916C>T|||||4749|,T|downstream_gene_variant|MODIFIER|NOTCH2NL|ENSG00000213240|transcript|ENST00000479995|processed_transcript||n.*4431C>T|||||4431|,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/16|c.175+2823C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-36+3135C>T|||||| GT:AD:AF:DP 0/1:217,8:0.052:225 0/0:98,6:0.082:104 | |
| chr1 145298168 . G A . PASS ClippingRankSum=0;DP=695;ECNT=1;FS=29.58;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=39.21;MQ0=93;MQRankSum=-1.377;NLOD=15.37;ReadPosRankSum=-1.685;TLOD=31.54;ANN=A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|5/84|c.580G>A|p.Ala194Thr|615/10697|580/10662|194/3553||,A|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|5/47|c.580G>A|p.Ala194Thr|615/5348|580/1797|194/598||,A|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|10/23|c.*687G>A|||||4972|,A|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|5/19|c.*285G>A|||||1795|,A|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|5/19|c.*285G>A|||||1795|,A|upstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding||c.-3569G>A|||||3567|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/16|c.176-3552G>A||||||,A|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|1/15|c.-35-1562G>A|||||| GT:AD:AF:DP 0/1:311,24:0.081:335 0/0:192,13:0.075:205 | |
| chr1 145299787 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2139;ECNT=2;FS=0;HCNT=2;MAX_ED=21;MIN_ED=21;MQ=36.83;MQ0=469;MQRankSum=0.921;NLOD=77.27;ReadPosRankSum=-1.347;TLOD=14.13;ANN=G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|6/84|c.836T>G|p.Leu279Trp|871/10697|836/10662|279/3553||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|2/16|c.23T>G|p.Leu8Trp|213/3715|23/2010|8/669||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|6/47|c.836T>G|p.Leu279Trp|871/5348|836/1797|279/598||,G|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|11/23|c.*943T>G|||||6591|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|6/19|c.*541T>G|||||3414|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|6/19|c.*541T>G|||||3414|,G|upstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding||c.-1950T>G|||||1948|WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/16|c.176-1933T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:868,13:0.013:881:0|1:145299787_T_G 0/0:572,4:0.005391:576:0|1:145299787_T_G | |
| chr1 145299808 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1983;ECNT=2;FS=0;HCNT=2;MAX_ED=21;MIN_ED=21;MQ=38.67;MQ0=385;MQRankSum=0.609;NLOD=83.64;ReadPosRankSum=2.185;TLOD=13.87;ANN=C|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|6/84|c.857T>C|p.Met286Thr|892/10697|857/10662|286/3553||,C|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|2/16|c.44T>C|p.Met15Thr|234/3715|44/2010|15/669||,C|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|6/47|c.857T>C|p.Met286Thr|892/5348|857/1797|286/598||,C|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|11/23|c.*964T>C|||||6612|,C|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|6/19|c.*562T>C|||||3435|,C|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|6/19|c.*562T>C|||||3435|,C|upstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding||c.-1929T>C|||||1927|WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|3/16|c.176-1912T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:855,12:0.012:867:0|1:145299787_T_G 0/0:528,4:0.005348:532:0|1:145299787_T_G | |
| chr1 145302714 . A G . PASS ClippingRankSum=0;DP=242;ECNT=1;FS=57.568;HCNT=41;MAX_ED=.;MIN_ED=.;MQ=40.13;MQ0=33;MQRankSum=-0.931;NLOD=6.28;ReadPosRankSum=-1.445;TLOD=12.40;ANN=G|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|8/84|c.1152A>G|p.Leu384Leu|1187/10697|1152/10662|384/3553||,G|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|5/17|c.339A>G|p.Leu113Leu|592/3888|339/2016|113/671||,G|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|4/16|c.339A>G|p.Leu113Leu|529/3715|339/2010|113/669||,G|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|8/47|c.1152A>G|p.Leu384Leu|1187/5348|1152/1797|384/598||,G|synonymous_variant|LOW|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|2/22|c.147A>G|p.Leu49Leu|149/3689|147/2781|49/926||WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|13/23|c.*1259A>G|||||9518|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|8/19|c.*857A>G|||||6341|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|8/19|c.*857A>G|||||6341| GT:AD:AF:DP 0/1:79,8:0.101:87 0/0:70,7:0.104:77 | |
| chr1 145303883 . C T . t_lod_fstar ClippingRankSum=0;DP=895;ECNT=1;FS=6.734;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=54.35;MQ0=28;MQRankSum=-3.993;NLOD=39.38;ReadPosRankSum=-3.253;TLOD=4.16;ANN=T|intron_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|13/22|c.*1414-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|8/83|c.1307-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|5/16|c.494-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|8/18|c.*1012-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|8/18|c.*1012-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|4/15|c.494-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|8/46|c.1307-27C>T||||||,T|intron_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|2/21|c.302-27C>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:594,8:0.019:602 0/0:242,6:0.029:248 | |
| chr1 145304595 . A G . PASS ClippingRankSum=0;DP=2423;ECNT=1;FS=1.291;HCNT=30;MAX_ED=.;MIN_ED=.;MQ=50.05;MQ0=185;MQRankSum=-1.267;NLOD=56.60;ReadPosRankSum=2.119;TLOD=16.94;ANN=G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding|10/84|c.1528A>G|p.Thr510Ala|1563/10697|1528/10662|510/3553||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|7/17|c.715A>G|p.Thr239Ala|968/3888|715/2016|239/671||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|6/16|c.715A>G|p.Thr239Ala|905/3715|715/2010|239/669||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay|10/47|c.1528A>G|p.Thr510Ala|1563/5348|1528/1797|510/598||,G|missense_variant|MODERATE|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|4/22|c.523A>G|p.Thr175Ala|525/3689|523/2781|175/926||WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|RP11-458D21.5|ENSG00000255168|transcript|ENST00000468030|nonsense_mediated_decay|15/23|c.*1635A>G|||||11399|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000464433|nonsense_mediated_decay|10/19|c.*1233A>G|||||8222|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding|10/19|c.*1233A>G|||||8222| GT:AD:AF:DP 0/1:1463,46:0.028:1509 0/0:610,69:0.095:679 | |
| chr1 145368695 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=853;ECNT=3;FS=5.237;HCNT=5;MAX_ED=12;MIN_ED=4;MQ=59.13;MQ0=2;MQRankSum=-7.096;NLOD=16.49;ReadPosRankSum=-4.897;TLOD=8.46;ANN=C|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|17/17|c.*11G>C|||||11|,C|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|16/16|c.*11G>C|||||11|,C|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|22/22|c.*11G>C|||||11|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding||c.*11G>C|||||11|,C|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000433081|lincRNA||n.*4359C>G|||||4359|,C|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding||c.*72322G>C|||||941|,C|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay||c.*52160G>C|||||4084|,C|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000457465|lincRNA||n.*4601C>G|||||4601|,C|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000421937|lincRNA||n.*4602C>G|||||4602| GT:AD:AF:DP:PGT:PID 0/1:567,6:0.012:573:0|1:145368695_G_C 0/0:253,13:0.065:266:0|1:145368695_G_C | |
| chr1 145368699 . T G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=820;ECNT=3;FS=2.814;HCNT=5;MAX_ED=12;MIN_ED=4;MQ=59.64;MQ0=2;MQRankSum=-8.861;NLOD=12.86;ReadPosRankSum=-2.125;TLOD=5.82;ANN=G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|17/17|c.*15T>G|||||15|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|16/16|c.*15T>G|||||15|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|22/22|c.*15T>G|||||15|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding||c.*15T>G|||||15|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000433081|lincRNA||n.*4355A>C|||||4355|,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding||c.*72326T>G|||||945|,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay||c.*52164T>G|||||4088|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000457465|lincRNA||n.*4597A>C|||||4597|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000421937|lincRNA||n.*4598A>C|||||4598| GT:AD:AF:DP:PGT:PID 0/1:557,3:0.007426:560:0|1:145368695_G_C 0/0:248,6:0.071:254:0|1:145368695_G_C | |
| chr1 145368707 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=758;ECNT=3;FS=2.794;HCNT=5;MAX_ED=12;MIN_ED=4;MQ=59.73;MQ0=2;MQRankSum=-12.926;NLOD=32.57;ReadPosRankSum=-2.864;TLOD=5.95;ANN=G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369339|protein_coding|17/17|c.*23A>G|||||23|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000369338|protein_coding|16/16|c.*23A>G|||||23|,G|3_prime_UTR_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000605176|protein_coding|22/22|c.*23A>G|||||23|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000342960|protein_coding||c.*23A>G|||||23|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000433081|lincRNA||n.*4347T>C|||||4347|,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000448873|protein_coding||c.*72334A>G|||||953|,G|downstream_gene_variant|MODIFIER|NBPF10|ENSG00000163386|transcript|ENST00000490598|nonsense_mediated_decay||c.*52172A>G|||||4096|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000457465|lincRNA||n.*4589T>C|||||4589|,G|downstream_gene_variant|MODIFIER|RP11-458D21.1|ENSG00000233396|transcript|ENST00000421937|lincRNA||n.*4590T>C|||||4590| GT:AD:AF:DP:PGT:PID 0/1:514,3:0.008197:517:0|1:145368695_G_C 0/0:232,5:0.035:237:0|1:145368695_G_C | |
| chr1 146013533 . G A . germline_risk ClippingRankSum=0;DP=316;ECNT=1;FS=0;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=52.23;MQ0=24;MQRankSum=-7.46;NLOD=0.511;ReadPosRankSum=1.849;TLOD=46.52;ANN=A|intron_variant|MODIFIER|RP11-94I2.1|ENSG00000229828|transcript|ENST00000420737|unprocessed_pseudogene|3/10|n.459-40G>A|||||| GT:AD:AF:DP 0/1:157,32:0.165:189 0/0:86,10:0.09:96 | |
| chr1 146215358 . A G . t_lod_fstar ClippingRankSum=0;DP=226;ECNT=1;FS=13.02;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=46.32;MQ0=9;MQRankSum=-1.543;NLOD=16.80;ReadPosRankSum=0.976;TLOD=4.22;ANN=G|intron_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000491285|transcribed_unprocessed_pseudogene|37/37|n.4829-40T>C||||||,G|intron_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000436832|transcribed_unprocessed_pseudogene|1/2|n.45-40T>C|||||| GT:AD:AF:DP 0/1:119,3:0.033:122 0/0:80,0:0:80 | |
| chr1 146250921 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1267;ECNT=2;FS=0;HCNT=4;MAX_ED=21;MIN_ED=21;MQ=36.89;MQ0=363;MQRankSum=-0.985;NLOD=45.40;ReadPosRankSum=2.083;TLOD=8.97;ANN=G|non_coding_transcript_exon_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000491285|transcribed_unprocessed_pseudogene|3/38|n.364T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000429672|transcribed_unprocessed_pseudogene|1/6|n.89T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:382,7:0.015:389:0|1:146250921_A_G 0/0:355,6:0.013:361:0|1:146250921_A_G | |
| chr1 146250942 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1097;ECNT=2;FS=0;HCNT=4;MAX_ED=21;MIN_ED=21;MQ=36.69;MQ0=339;MQRankSum=-1.773;NLOD=38.31;ReadPosRankSum=0.999;TLOD=9.26;ANN=C|non_coding_transcript_exon_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000491285|transcribed_unprocessed_pseudogene|3/38|n.343T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|WI2-3658N16.1|ENSG00000232637|transcript|ENST00000429672|transcribed_unprocessed_pseudogene|1/6|n.68T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:298,7:0.018:305:0|1:146250921_A_G 0/0:321,4:0.017:325:0|1:146250921_A_G | |
| chr1 146395423 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=857;ECNT=3;FS=7.567;HCNT=13;MAX_ED=48;MIN_ED=40;MQ=37.87;MQ0=409;MQRankSum=1.345;NLOD=23.84;ReadPosRankSum=-0.207;TLOD=5.69;ANN=C|synonymous_variant|LOW|NBPF12|ENSG00000186275|transcript|ENST00000442909|protein_coding|5/82|c.82T>C|p.Leu28Leu|918/12455|82/9996|28/3331||,C|synonymous_variant|LOW|NBPF12|ENSG00000186275|transcript|ENST00000446760|protein_coding|7/29|c.82T>C|p.Leu28Leu|1381/5560|82/2517|28/838||,C|5_prime_UTR_premature_start_codon_gain_variant|LOW|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|5/25|c.-41T>C||||||,C|5_prime_UTR_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|5/25|c.-41T>C|||||41|,C|TF_binding_site_variant|MODIFIER|||CTCF|MA0139.1|||n.146395423A>G||||||,C|upstream_gene_variant|MODIFIER|PFN1P8|ENSG00000244371|transcript|ENST00000497012|processed_pseudogene||n.-2571A>G|||||2571| GT:AD:AF:DP 0/1:158,5:0.034:163 0/0:245,21:0.078:266 | |
| chr1 146395463 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=846;ECNT=3;FS=10.363;HCNT=8;MAX_ED=48;MIN_ED=40;MQ=42.42;MQ0=277;MQRankSum=1.248;NLOD=21.42;ReadPosRankSum=-4.034;TLOD=6.23;ANN=A|missense_variant|MODERATE|NBPF12|ENSG00000186275|transcript|ENST00000442909|protein_coding|5/82|c.122G>A|p.Arg41Lys|958/12455|122/9996|41/3331||,A|missense_variant|MODERATE|NBPF12|ENSG00000186275|transcript|ENST00000446760|protein_coding|7/29|c.122G>A|p.Arg41Lys|1421/5560|122/2517|41/838||,A|5_prime_UTR_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|5/25|c.-1G>A|||||1|,A|upstream_gene_variant|MODIFIER|PFN1P8|ENSG00000244371|transcript|ENST00000497012|processed_pseudogene||n.-2611C>T|||||2611| GT:AD:AF:DP:PGT:PID 0/1:260,3:0.017:263:0|1:146395463_G_A 0/0:260,14:0.063:274:0|1:146395463_G_A | |
| chr1 146395471 . C G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=836;ECNT=3;FS=13.558;HCNT=8;MAX_ED=48;MIN_ED=40;MQ=42.59;MQ0=266;MQRankSum=0.399;NLOD=21.72;ReadPosRankSum=-2.473;TLOD=6.21;ANN=G|missense_variant|MODERATE|NBPF12|ENSG00000186275|transcript|ENST00000442909|protein_coding|5/82|c.130C>G|p.Leu44Val|966/12455|130/9996|44/3331||,G|missense_variant|MODERATE|NBPF12|ENSG00000186275|transcript|ENST00000446760|protein_coding|7/29|c.130C>G|p.Leu44Val|1429/5560|130/2517|44/838||,G|missense_variant|MODERATE|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|5/25|c.8C>G|p.Ser3Cys|671/3409|8/2373|3/790||,G|upstream_gene_variant|MODIFIER|PFN1P8|ENSG00000244371|transcript|ENST00000497012|processed_pseudogene||n.-2619G>C|||||2619| GT:AD:AF:DP:PGT:PID 0/1:263,3:0.017:266:0|1:146395463_G_A 0/0:263,9:0.059:272:0|1:146395463_G_A | |
| chr1 146397444 . A G . t_lod_fstar ClippingRankSum=0;DP=108;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=56.16;MQ0=8;MQRankSum=-7.169;NLOD=4.77;ReadPosRankSum=2.27;TLOD=4.06;ANN=G|synonymous_variant|LOW|NBPF12|ENSG00000186275|transcript|ENST00000442909|protein_coding|6/82|c.261A>G|p.Lys87Lys|1097/12455|261/9996|87/3331||,G|synonymous_variant|LOW|NBPF12|ENSG00000186275|transcript|ENST00000446760|protein_coding|8/29|c.261A>G|p.Lys87Lys|1560/5560|261/2517|87/838||,G|upstream_gene_variant|MODIFIER|PFN1P8|ENSG00000244371|transcript|ENST00000497012|processed_pseudogene||n.-4592T>C|||||4592|,G|intron_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|5/24|c.54-849A>G|||||| GT:AD:AF:DP 0/1:73,4:0.053:77 0/0:20,1:0.059:21 | |
| chr1 146403789 . G A . t_lod_fstar ClippingRankSum=0;DP=168;ECNT=1;FS=4.936;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=40.81;MQ0=38;MQRankSum=-1.689;NLOD=5.72;ReadPosRankSum=-0.602;TLOD=6.15;ANN=A|upstream_gene_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000439206|protein_coding||c.-8885G>A|||||807|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000442909|protein_coding|11/81|c.1091+32G>A||||||,A|intron_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000446760|protein_coding|11/28|c.616-2650G>A||||||,A|intron_variant|MODIFIER|NBPF12|ENSG00000186275|transcript|ENST00000309471|protein_coding|8/24|c.391-2650G>A|||||| GT:AD:AF:DP 0/1:84,4:0.056:88 0/0:34,1:0.042:35 | |
| chr1 147597264 . G C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=571;ECNT=2;FS=3.312;HCNT=31;MAX_ED=78;MIN_ED=78;MQ=35.32;MQ0=233;MQRankSum=-2.993;NLOD=1.57;ReadPosRankSum=0.701;TLOD=9.62;ANN=C|missense_variant|MODERATE|NBPF24|ENSG00000203836|transcript|ENST00000369228|protein_coding|3/21|c.196C>G|p.Leu66Val|357/2995|196/2598|66/865||,C|missense_variant|MODERATE|NBPF24|ENSG00000203836|transcript|ENST00000474625|nonsense_mediated_decay|7/25|c.196C>G|p.Leu66Val|1495/4407|196/1797|66/598||,C|upstream_gene_variant|MODIFIER|PFN1P4|ENSG00000225080|transcript|ENST00000450970|processed_pseudogene||n.-4516G>C|||||4516|,C|upstream_gene_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000469181|processed_transcript||n.-651C>G|||||651|,C|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000480568|nonsense_mediated_decay|5/22|c.54-914C>G||||||,C|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000369226|protein_coding|5/22|c.54-914C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000470042|processed_transcript|6/7|n.798C>G|||||| GT:AD:AF:DP 0/1:115,12:0.095:127 0/0:156,6:0.032:162 | |
| chr1 147597342 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=514;ECNT=2;FS=0;HCNT=38;MAX_ED=78;MIN_ED=78;MQ=33.99;MQ0=277;MQRankSum=-3.595;NLOD=3.04;ReadPosRankSum=-0.201;TLOD=5.38;ANN=T|upstream_gene_variant|MODIFIER|PFN1P4|ENSG00000225080|transcript|ENST00000450970|processed_pseudogene||n.-4438C>T|||||4438|,T|upstream_gene_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000469181|processed_transcript||n.-729G>A|||||729|,T|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000369228|protein_coding|2/20|c.176-58G>A||||||,T|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000480568|nonsense_mediated_decay|5/22|c.54-992G>A||||||,T|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000474625|nonsense_mediated_decay|6/24|c.176-58G>A||||||,T|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000369226|protein_coding|5/22|c.54-992G>A||||||,T|intron_variant|MODIFIER|NBPF24|ENSG00000203836|transcript|ENST00000470042|processed_transcript|5/6|n.778-58G>A|||||| GT:AD:AF:DP 0/1:46,6:0.093:52 0/0:152,3:0.022:155 | |
| chr1 148004525 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=677;ECNT=8;FS=5.712;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=54.2;MQ0=27;MQRankSum=-2.542;NLOD=12.03;ReadPosRankSum=-1.133;TLOD=14.41;ANN=T|3_prime_UTR_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.*23G>A|||||23|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.*23G>A|||||23|,T|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4031C>T|||||4031|,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*941G>A|||||941|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:406,6:0.021:412:0|1:148004525_C_T 0/0:204,7:0.047:211:0|1:148004525_C_T | |
| chr1 148004548 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=785;ECNT=8;FS=3.271;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=52.59;MQ0=32;MQRankSum=-4.955;NLOD=9.71;ReadPosRankSum=-3.416;TLOD=44.42;ANN=C|stop_retained_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2781A>G|p.Ter927Ter|2783/3689|2781/2781|927/926||WARNING_TRANSCRIPT_NO_START_CODON,C|stop_retained_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2766A>G|p.Ter922Ter|2783/3671|2766/2766|922/921||,C|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4054T>C|||||4054|,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*918A>G|||||918|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:450,20:0.05:470:0|1:148004525_C_T 0/0:232,12:0.051:244:0|1:148004525_C_T | |
| chr1 148004567 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=858;ECNT=8;FS=1.202;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=51.4;MQ0=51;MQRankSum=-4.543;NLOD=7.08;ReadPosRankSum=-2.451;TLOD=46.38;ANN=A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2762G>T|p.Gly921Val|2764/3689|2762/2781|921/926||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2747G>T|p.Gly916Val|2764/3671|2747/2766|916/921||,A|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4073C>A|||||4073|,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*899G>T|||||899|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:471,24:0.051:495:0|1:148004525_C_T 0/0:254,17:0.061:271:0|1:148004525_C_T | |
| chr1 148004568 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=862;ECNT=8;FS=1.215;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=51.35;MQ0=51;MQRankSum=-4.522;NLOD=7.08;ReadPosRankSum=-2.196;TLOD=46.33;ANN=A|stop_gained|HIGH|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2761G>T|p.Gly921*|2763/3689|2761/2781|921/926||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2746G>T|p.Gly916*|2763/3671|2746/2766|916/921||,A|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4074C>A|||||4074|,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*898G>T|||||898|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:472,24:0.051:496:0|1:148004525_C_T 0/0:256,17:0.06:273:0|1:148004525_C_T | |
| chr1 148004584 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=890;ECNT=8;FS=0;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=50.7;MQ0=52;MQRankSum=-4.881;NLOD=10.53;ReadPosRankSum=-1.108;TLOD=48.05;ANN=A|synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2745C>T|p.His915His|2747/3689|2745/2781|915/926||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2730C>T|p.His910His|2747/3671|2730/2766|910/921||,A|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4090G>A|||||4090|,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:475,32:0.055:507:0|1:148004525_C_T 0/0:265,20:0.059:285:0|1:148004525_C_T | |
| chr1 148004625 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=796;ECNT=8;FS=1.055;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=50.45;MQ0=45;MQRankSum=-4.868;NLOD=16.26;ReadPosRankSum=4.592;TLOD=23.46;ANN=A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2704G>T|p.Val902Leu|2706/3689|2704/2781|902/926||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2689G>T|p.Val897Leu|2706/3671|2689/2766|897/921||,A|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4131C>A|||||4131|,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*841G>T|||||841|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:428,33:0.051:461 0/0:234,18:0.061:252 | |
| chr1 148004644 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=662;ECNT=8;FS=30.741;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=50.12;MQ0=45;MQRankSum=-6.013;NLOD=17.62;ReadPosRankSum=-4.717;TLOD=81.18;ANN=G|synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2685T>C|p.His895His|2687/3689|2685/2781|895/926||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2670T>C|p.His890His|2687/3671|2670/2766|890/921||,G|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4150A>G|||||4150|,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*822T>C|||||822|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:339,29:0.103:368:0|1:148004644_A_G 0/0:201,11:0.065:212:0|1:148004644_A_G | |
| chr1 148004649 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=644;ECNT=8;FS=27.866;HCNT=4;MAX_ED=124;MIN_ED=23;MQ=50.08;MQ0=44;MQRankSum=-6.323;NLOD=21.17;ReadPosRankSum=-4.798;TLOD=78.86;ANN=G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|22/22|c.2680G>C|p.Glu894Gln|2682/3689|2680/2781|894/926||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|22/22|c.2665G>C|p.Glu889Gln|2682/3671|2665/2766|889/921||,G|downstream_gene_variant|MODIFIER|RP3-328E19.4|ENSG00000223491|transcript|ENST00000416378|processed_pseudogene||n.*4155C>G|||||4155|,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding||c.*817G>C|||||817|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:335,27:0.101:362:0|1:148004644_A_G 0/0:196,8:0.054:204:0|1:148004644_A_G | |
| chr1 148016476 . G T . t_lod_fstar ClippingRankSum=0;DP=1518;ECNT=1;FS=5.004;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=42.92;MQ0=201;MQRankSum=1.487;NLOD=57.98;ReadPosRankSum=-4.961;TLOD=6.10;ANN=T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|6/21|c.797-16C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|6/21|c.782-16C>A||||||,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|6/12|c.812-16C>A||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:858,12:0.018:870 0/0:411,20:0.061:431 | |
| chr1 148017686 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=742;ECNT=2;FS=7.959;HCNT=4;MAX_ED=7;MIN_ED=7;MQ=54.83;MQ0=23;MQRankSum=-2.528;NLOD=13.92;ReadPosRankSum=-5.708;TLOD=11.00;ANN=C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|5/21|c.633-21C>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|5/21|c.618-21C>G||||||,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|5/12|c.648-21C>G||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:443,9:0.025:452:0|1:148017686_G_C 0/0:225,13:0.07:238:0|1:148017686_G_C | |
| chr1 148017693 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=662;ECNT=2;FS=5.402;HCNT=4;MAX_ED=7;MIN_ED=7;MQ=56.38;MQ0=15;MQRankSum=-1.452;NLOD=14.41;ReadPosRankSum=-4.525;TLOD=7.12;ANN=T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|5/21|c.633-28G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|5/21|c.618-28G>A||||||,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|5/12|c.648-28G>A||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP:PGT:PID 0/1:398,3:0.013:401:0|1:148017686_G_C 0/0:214,7:0.068:221:0|1:148017686_G_C | |
| chr1 148022984 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1954;ECNT=3;FS=0.994;HCNT=7;MAX_ED=140;MIN_ED=83;MQ=41.74;MQ0=427;MQRankSum=-1.152;NLOD=7.75;ReadPosRankSum=8.867;TLOD=24.36;ANN=C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|4/22|c.523A>G|p.Thr175Ala|525/3689|523/2781|175/926||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|4/22|c.508A>G|p.Thr170Ala|525/3671|508/2766|170/921||,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|4/13|c.538A>G|p.Thr180Ala|540/1534|538/1532|180/509||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:805,48:0.044:853 0/0:488,71:0.112:559 | |
| chr1 148023067 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2214;ECNT=3;FS=14.759;HCNT=6;MAX_ED=140;MIN_ED=83;MQ=37.14;MQ0=448;MQRankSum=0.77;NLOD=21.54;ReadPosRankSum=-4.384;TLOD=34.66;ANN=T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|4/22|c.440G>A|p.Cys147Tyr|442/3689|440/2781|147/926||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|4/22|c.425G>A|p.Cys142Tyr|442/3671|425/2766|142/921||,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|4/13|c.455G>A|p.Cys152Tyr|457/1534|455/1532|152/509||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:966,40:0.059:1006 0/0:530,64:0.12:594 | |
| chr1 148023124 . T G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1413;ECNT=3;FS=26.217;HCNT=4;MAX_ED=140;MIN_ED=83;MQ=37.84;MQ0=160;MQRankSum=1.044;NLOD=39.12;ReadPosRankSum=0.769;TLOD=19.36;ANN=G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|4/22|c.383A>C|p.Gln128Pro|385/3689|383/2781|128/926||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|4/22|c.368A>C|p.Gln123Pro|385/3671|368/2766|123/921||,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|4/13|c.398A>C|p.Gln133Pro|400/1534|398/1532|133/509||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:710,22:0.042:732 0/0:362,15:0.052:377 | |
| chr1 148025702 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=631;ECNT=3;FS=0;HCNT=20;MAX_ED=95;MIN_ED=61;MQ=41.86;MQ0=89;MQRankSum=1.034;NLOD=8.13;ReadPosRankSum=-2.034;TLOD=13.29;ANN=A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|1/21|c.86+59C>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|1/21|c.71+59C>T||||||,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|1/12|c.101+59C>T||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:303,12:0.043:315 0/0:153,14:0.077:167 | |
| chr1 148025763 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=633;ECNT=3;FS=8.391;HCNT=22;MAX_ED=95;MIN_ED=61;MQ=43.35;MQ0=87;MQRankSum=1.918;NLOD=7.71;ReadPosRankSum=2.855;TLOD=15.46;ANN=A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|1/22|c.84C>T|p.Leu28Leu|86/3689|84/2781|28/926||WARNING_TRANSCRIPT_NO_START_CODON,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|1/22|c.69C>T|p.Leu23Leu|86/3671|69/2766|23/921||,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE,A|splice_region_variant&synonymous_variant|LOW|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|1/13|c.99C>T|p.Leu33Leu|101/1534|99/1532|33/509||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:266,12:0.047:278 0/0:169,24:0.145:193 | |
| chr1 148025797 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=568;ECNT=3;FS=0;HCNT=23;MAX_ED=95;MIN_ED=61;MQ=46.1;MQ0=58;MQRankSum=-0.932;NLOD=11.29;ReadPosRankSum=-0.722;TLOD=12.03;ANN=A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000310701|protein_coding|1/22|c.50A>T|p.Lys17Met|52/3689|50/2781|17/926||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000369219|protein_coding|1/22|c.35A>T|p.Lys12Met|52/3671|35/2766|12/921||,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000392972|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000431121|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000436356|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000444640|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000448574|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000458135|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF14|ENSG00000122497|transcript|ENST00000426874|protein_coding|1/13|c.65A>T|p.Lys22Met|67/1534|65/1532|22/509||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:258,11:0.038:269 0/0:155,11:0.081:166 | |
| chr1 148251852 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=459;ECNT=2;FS=20.965;HCNT=2;MAX_ED=22;MIN_ED=22;MQ=57.93;MQ0=18;MQRankSum=-6.666;NLOD=4.60;ReadPosRankSum=-4.122;TLOD=26.13;ANN=C|3_prime_UTR_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|111/111|c.*23A>G|||||23|,C|upstream_gene_variant|MODIFIER|RP11-89F3.2|ENSG00000236140|transcript|ENST00000427732|lincRNA||n.-3748A>G|||||3748| GT:AD:AF:DP:PGT:PID 0/1:280,9:0.049:289:0|1:148251852_T_C 0/0:132,17:0.161:149:0|1:148251852_T_C | |
| chr1 148251874 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=539;ECNT=2;FS=15.138;HCNT=2;MAX_ED=22;MIN_ED=22;MQ=57.05;MQ0=20;MQRankSum=-3.53;NLOD=7.57;ReadPosRankSum=-0.567;TLOD=25.59;ANN=C|3_prime_UTR_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|111/111|c.*1A>G|||||1|,C|upstream_gene_variant|MODIFIER|RP11-89F3.2|ENSG00000236140|transcript|ENST00000427732|lincRNA||n.-3770A>G|||||3770| GT:AD:AF:DP:PGT:PID 0/1:326,10:0.043:336:0|1:148251852_T_C 0/0:153,24:0.155:177:0|1:148251852_T_C | |
| chr1 148342535 . G A . t_lod_fstar ClippingRankSum=0;DP=869;ECNT=1;FS=3.522;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=56.39;MQ0=33;MQRankSum=-3.943;NLOD=52.01;ReadPosRankSum=-1.023;TLOD=5.79;ANN=A|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|5/111|c.501C>T|p.Asp167Asp|699/15690|501/13866|167/4621||,A|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|5/20|c.501C>T|p.Asp167Asp|580/2604|501/2525|167/840||WARNING_TRANSCRIPT_INCOMPLETE,A|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|4/19|c.276C>T|p.Asp92Asp|1051/3072|276/2297|92/764||WARNING_TRANSCRIPT_INCOMPLETE,A|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|4/5|c.501C>T|p.Asp167Asp|674/950|501/777|167/258||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:498,5:0.014:503 0/0:309,5:0.017:314 | |
| chr1 148343676 . G T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=464;ECNT=3;FS=12.161;HCNT=19;MAX_ED=116;MIN_ED=3;MQ=40.95;MQ0=87;MQRankSum=-0.102;NLOD=18.04;ReadPosRankSum=-3.019;TLOD=5.65;ANN=T|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|4/111|c.411C>A|p.Asp137Glu|609/15690|411/13866|137/4621||,T|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|4/20|c.411C>A|p.Asp137Glu|490/2604|411/2525|137/840||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|3/19|c.186C>A|p.Asp62Glu|961/3072|186/2297|62/764||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|3/5|c.411C>A|p.Asp137Glu|584/950|411/777|137/258||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:200,3:0.019:203:0|1:148343676_G_T 0/0:145,2:0.018:147:0|1:148343676_G_T | |
| chr1 148343679 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=469;ECNT=3;FS=9.101;HCNT=19;MAX_ED=116;MIN_ED=3;MQ=41.4;MQ0=85;MQRankSum=0.16;NLOD=17.49;ReadPosRankSum=-2.651;TLOD=4.37;ANN=T|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|4/111|c.408G>A|p.Pro136Pro|606/15690|408/13866|136/4621||,T|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|4/20|c.408G>A|p.Pro136Pro|487/2604|408/2525|136/840||WARNING_TRANSCRIPT_INCOMPLETE,T|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|3/19|c.183G>A|p.Pro61Pro|958/3072|183/2297|61/764||WARNING_TRANSCRIPT_INCOMPLETE,T|synonymous_variant|LOW|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|3/5|c.408G>A|p.Pro136Pro|581/950|408/777|136/258||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:203,2:0.013:205:0|1:148343676_G_T 0/0:151,2:0.019:153:0|1:148343676_G_T | |
| chr1 148343792 . C A . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=585;ECNT=3;FS=0;HCNT=19;MAX_ED=116;MIN_ED=3;MQ=48.83;MQ0=46;MQRankSum=-5.169;NLOD=1.44;ReadPosRankSum=7.33;TLOD=44.96;ANN=A|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|4/111|c.295G>T|p.Val99Phe|493/15690|295/13866|99/4621||,A|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|4/20|c.295G>T|p.Val99Phe|374/2604|295/2525|99/840||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|3/19|c.70G>T|p.Val24Phe|845/3072|70/2297|24/764||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|3/5|c.295G>T|p.Val99Phe|468/950|295/777|99/258||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:277,43:0.107:320 0/0:175,18:0.079:193 | |
| chr1 148344615 . G GC . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=377;ECNT=2;FS=5.571;HCNT=9;MAX_ED=107;MIN_ED=107;MQ=47.22;MQ0=28;MQRankSum=-1.359;NLOD=4.69;ReadPosRankSum=1.039;TLOD=20.34;ANN=GC|upstream_gene_variant|MODIFIER|PFN1P3|ENSG00000234367|transcript|ENST00000443612|processed_pseudogene||n.-4641_-4640insC|||||4640|,GC|intron_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|3/110|c.278+24dupG||||||,GC|intron_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|3/19|c.278+24dupG||||||WARNING_TRANSCRIPT_INCOMPLETE,GC|intron_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|2/18|c.54-808dupG||||||WARNING_TRANSCRIPT_INCOMPLETE,GC|intron_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|2/4|c.278+24dupG||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:182,18:0.077:200 0/0:104,6:0.071:110 | |
| chr1 148344722 . G C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=350;ECNT=2;FS=1.128;HCNT=10;MAX_ED=107;MIN_ED=107;MQ=46.24;MQ0=33;MQRankSum=-0.925;NLOD=16.51;ReadPosRankSum=-3.549;TLOD=4.70;ANN=C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|3/111|c.196C>G|p.Leu66Val|394/15690|196/13866|66/4621||,C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|3/20|c.196C>G|p.Leu66Val|275/2604|196/2525|66/840||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|2/5|c.196C>G|p.Leu66Val|369/950|196/777|66/258||WARNING_TRANSCRIPT_NO_STOP_CODON,C|upstream_gene_variant|MODIFIER|PFN1P3|ENSG00000234367|transcript|ENST00000443612|processed_pseudogene||n.-4534G>C|||||4534|,C|intron_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|2/18|c.54-914C>G||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:199,11:0.037:210 0/0:87,1:0.015:88 | |
| chr1 148346627 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=573;ECNT=2;FS=15.279;HCNT=30;MAX_ED=122;MIN_ED=122;MQ=54.7;MQ0=38;MQRankSum=-6.858;NLOD=19.43;ReadPosRankSum=-4.905;TLOD=14.30;ANN=G|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|2/111|c.130G>C|p.Val44Leu|328/15690|130/13866|44/4621||,G|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|2/20|c.130G>C|p.Val44Leu|209/2604|130/2525|44/840||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|2/19|c.8G>C|p.Cys3Ser|783/3072|8/2297|3/764||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|1/5|c.130G>C|p.Val44Leu|303/950|130/777|44/258||WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|PFN1P3|ENSG00000234367|transcript|ENST00000443612|processed_pseudogene||n.-2629C>G|||||2629| GT:AD:AF:DP 0/1:342,13:0.05:355 0/0:164,5:0.04:169 | |
| chr1 148346749 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=631;ECNT=2;FS=3.742;HCNT=24;MAX_ED=122;MIN_ED=122;MQ=41.07;MQ0=161;MQRankSum=-1.216;NLOD=26.21;ReadPosRankSum=-0.44;TLOD=6.70;ANN=C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369202|protein_coding|2/111|c.8T>G|p.Val3Gly|206/15690|8/13866|3/4621||,C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000369188|protein_coding|2/20|c.8T>G|p.Val3Gly|87/2604|8/2525|3/840||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|NBPF20|ENSG00000203832|transcript|ENST00000414710|protein_coding|1/5|c.8T>G|p.Val3Gly|181/950|8/777|3/258||WARNING_TRANSCRIPT_NO_STOP_CODON,C|5_prime_UTR_variant|MODIFIER|NBPF20|ENSG00000203832|transcript|ENST00000369189|protein_coding|2/19|c.-115T>G|||||115|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PFN1P3|ENSG00000234367|transcript|ENST00000443612|processed_pseudogene||n.-2507A>C|||||2507| GT:AD:AF:DP 0/1:251,8:0.04:259 0/0:180,8:0.039:188 | |
| chr1 148579625 . T C . germline_risk;t_lod_fstar ClippingRankSum=0;DP=303;ECNT=1;FS=1.354;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=37.63;MQ0=129;MQRankSum=0.017;NLOD=0.543;ReadPosRankSum=-3.634;TLOD=4.97;ANN=C|synonymous_variant|LOW|NBPF15|ENSG00000243452|transcript|ENST00000369187|protein_coding|6/19|c.195T>C|p.Asp65Asp|684/4125|195/2013|65/670||,C|synonymous_variant|LOW|NBPF15|ENSG00000243452|transcript|ENST00000442702|protein_coding|8/21|c.195T>C|p.Asp65Asp|1262/4707|195/2013|65/670||,C|upstream_gene_variant|MODIFIER|PFN1P7|ENSG00000227212|transcript|ENST00000476786|processed_pseudogene||n.-4574A>G|||||4574|,C|downstream_gene_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000488031|processed_transcript||n.*1965T>C|||||1965|,C|non_coding_transcript_exon_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000464336|processed_transcript|11/23|n.1789T>C|||||| GT:AD:AF:DP 0/1:74,4:0.058:78 0/0:75,8:0.104:83 | |
| chr1 148588954 . ACTG A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=2236;ECNT=2;FS=7.534;HCNT=8;MAX_ED=47;MIN_ED=47;MQ=35.72;MQ0=709;MQRankSum=4.42;NLOD=15.92;ReadPosRankSum=0.664;TLOD=38.91;ANN=A|intron_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000369187|protein_coding|11/18|c.989-37_989-35delGCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000464336|processed_transcript|16/22|n.2583-37_2583-35delGCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000442702|protein_coding|13/20|c.989-37_989-35delGCT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:729,17:0.028:746 0/0:617,61:0.104:678 | |
| chr1 148589001 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=3134;ECNT=2;FS=1.202;HCNT=5;MAX_ED=47;MIN_ED=47;MQ=34.62;MQ0=1166;MQRankSum=4.102;NLOD=56.05;ReadPosRankSum=-5.322;TLOD=9.47;ANN=C|synonymous_variant|LOW|NBPF15|ENSG00000243452|transcript|ENST00000369187|protein_coding|12/19|c.996G>C|p.Arg332Arg|1485/4125|996/2013|332/670||,C|synonymous_variant|LOW|NBPF15|ENSG00000243452|transcript|ENST00000442702|protein_coding|14/21|c.996G>C|p.Arg332Arg|2063/4707|996/2013|332/670||,C|non_coding_transcript_exon_variant|MODIFIER|NBPF15|ENSG00000243452|transcript|ENST00000464336|processed_transcript|17/23|n.2590G>C|||||| GT:AD:AF:DP 0/1:903,27:0.028:930 0/0:830,79:0.088:909 | |
| chr1 148873398 . C A . PASS ClippingRankSum=0;DP=1680;ECNT=1;FS=1.169;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=40.53;MQ0=404;MQRankSum=-2.674;NLOD=44.09;ReadPosRankSum=0.467;TLOD=69.04;ANN=A|splice_region_variant&intron_variant|LOW|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|1/9|n.25-8C>A|||||| GT:AD:AF:DP 0/1:655,53:0.075:708 0/0:472,21:0.04:493 | |
| chr1 148876254 . T A . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=505;ECNT=3;FS=0;HCNT=4;MAX_ED=109;MIN_ED=89;MQ=38.09;MQ0=226;MQRankSum=-2.206;NLOD=1.49;ReadPosRankSum=0.257;TLOD=19.20;ANN=A|intron_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|2/9|n.142-24T>A|||||| GT:AD:AF:DP 0/1:95,22:0.143:117 0/0:123,27:0.15:150 | |
| chr1 148876343 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1008;ECNT=3;FS=8.022;HCNT=3;MAX_ED=109;MIN_ED=89;MQ=32.3;MQ0=620;MQRankSum=3.189;NLOD=6.42;ReadPosRankSum=1.267;TLOD=18.77;ANN=A|non_coding_transcript_exon_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|3/10|n.207G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:123,8:0.061:131:0|1:148876343_G_A 0/0:187,53:0.215:240:0|1:148876343_G_A | |
| chr1 148876363 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1139;ECNT=3;FS=2.93;HCNT=3;MAX_ED=109;MIN_ED=89;MQ=34.82;MQ0=638;MQRankSum=3.7;NLOD=9.13;ReadPosRankSum=2.966;TLOD=16.31;ANN=A|non_coding_transcript_exon_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|3/10|n.227G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:195,6:0.043:201:0|1:148876343_G_A 0/0:224,51:0.199:275:0|1:148876343_G_A | |
| chr1 148882328 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1119;ECNT=3;FS=6.086;HCNT=6;MAX_ED=34;MIN_ED=5;MQ=43.51;MQ0=163;MQRankSum=0.215;NLOD=56.92;ReadPosRankSum=1.969;TLOD=15.90;ANN=G|non_coding_transcript_exon_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|5/10|n.510A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:566,7:0.016:573:0|1:148882328_A_G 0/0:341,12:0.045:353:0|1:148882328_A_G | |
| chr1 148882333 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1124;ECNT=3;FS=9.231;HCNT=6;MAX_ED=34;MIN_ED=5;MQ=43.31;MQ0=167;MQRankSum=0.216;NLOD=55.11;ReadPosRankSum=2.974;TLOD=15.94;ANN=T|non_coding_transcript_exon_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|5/10|n.515G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:565,7:0.016:572:0|1:148882328_A_G 0/0:340,12:0.046:352:0|1:148882328_A_G | |
| chr1 148882362 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1098;ECNT=3;FS=12.718;HCNT=7;MAX_ED=34;MIN_ED=5;MQ=43.06;MQ0=160;MQRankSum=0.377;NLOD=57.75;ReadPosRankSum=4.225;TLOD=4.51;ANN=T|non_coding_transcript_exon_variant|MODIFIER|RP11-763B22.9|ENSG00000231448|transcript|ENST00000444424|unprocessed_pseudogene|5/10|n.544C>T|||||| GT:AD:AF:DP 0/1:530,7:0.018:537 0/0:342,13:0.045:355 | |
| chr1 148903226 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=449;ECNT=2;FS=0;HCNT=7;MAX_ED=149;MIN_ED=149;MQ=50.93;MQ0=20;MQRankSum=-2.363;NLOD=2.32;ReadPosRankSum=-1.327;TLOD=24.76;ANN=A|downstream_gene_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000535197|processed_pseudogene||n.*123G>A|||||123|,A|downstream_gene_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000309892|processed_pseudogene||n.*313G>A|||||313|,A|non_coding_transcript_exon_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000421395|processed_pseudogene|2/2|n.1523G>A|||||| GT:AD:AF:DP 0/1:224,19:0.083:243 0/0:153,18:0.107:171 | |
| chr1 148903375 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=321;ECNT=2;FS=19.861;HCNT=7;MAX_ED=149;MIN_ED=149;MQ=52.38;MQ0=18;MQRankSum=-1.754;NLOD=4.26;ReadPosRankSum=2.562;TLOD=12.83;ANN=T|downstream_gene_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000535197|processed_pseudogene||n.*272C>T|||||272|,T|downstream_gene_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000309892|processed_pseudogene||n.*462C>T|||||462|,T|non_coding_transcript_exon_variant|MODIFIER|DRD5P2|ENSG00000175658|transcript|ENST00000421395|processed_pseudogene|2/2|n.1672C>T|||||| GT:AD:AF:DP 0/1:174,10:0.081:184 0/0:83,16:0.16:99 | |
| chr1 148934807 . T A . PASS ClippingRankSum=0;DP=1157;ECNT=1;FS=0;HCNT=31;MAX_ED=.;MIN_ED=.;MQ=47.34;MQ0=50;MQRankSum=1.762;NLOD=3.77;ReadPosRankSum=-1.432;TLOD=40.80;ANN=A|downstream_gene_variant|MODIFIER|RP11-14N7.2|ENSG00000232527|transcript|ENST00000420597|lincRNA||n.*1887T>A|||||1887|,A|downstream_gene_variant|MODIFIER|RP11-14N7.2|ENSG00000232527|transcript|ENST00000294715|lincRNA||n.*1439T>A|||||1439|,A|downstream_gene_variant|MODIFIER|RP11-14N7.2|ENSG00000232527|transcript|ENST00000457390|lincRNA||n.*1228T>A|||||1228|,A|intron_variant|MODIFIER|RP11-14N7.2|ENSG00000232527|transcript|ENST00000539543|lincRNA|3/3|n.254+1439T>A||||||,A|intron_variant|MODIFIER|RP11-14N7.2|ENSG00000232527|transcript|ENST00000452399|lincRNA|2/2|n.199+1887T>A|||||| GT:AD:AF:DP 0/1:652,38:0.053:690 0/0:357,30:0.088:387 | |
| chr1 149576741 . C T . PASS ClippingRankSum=0;DP=477;ECNT=1;FS=7.826;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=44.98;MQ0=26;MQRankSum=-1.401;NLOD=12.52;ReadPosRankSum=-1.157;TLOD=8.30;ANN=T|upstream_gene_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000598569|processed_transcript||n.-3783C>T|||||3783|,T|upstream_gene_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000594630|processed_transcript||n.-170C>T|||||170|,T|downstream_gene_variant|MODIFIER|RP11-277L2.4|ENSG00000268544|transcript|ENST00000596960|lincRNA||n.*974C>T|||||974|,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000417986|processed_transcript|2/2|n.185+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000593370|processed_transcript|2/2|n.337+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000434047|processed_transcript|2/2|n.305+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000444581|retained_intron|1/1|n.251+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000455295|processed_transcript|1/1|n.229+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000453293|processed_transcript|1/1|n.210+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000443884|processed_transcript|1/2|n.146+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000452356|transcribed_unprocessed_pseudogene|1/1|n.88+41C>T||||||,T|intron_variant|MODIFIER|RP11-353N4.6|ENSG00000269501|transcript|ENST00000419105|processed_transcript|1/3|n.68+41C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-277L2.3|ENSG00000233368|transcript|ENST00000447883|lincRNA|2/2|n.411G>A|||||| GT:AD:AF:DP 0/1:278,8:0.04:286 0/0:141,5:0.046:146 | |
| chr1 149676264 . T C . PASS ClippingRankSum=0;DP=379;ECNT=1;FS=3.584;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=52.75;MQ0=3;MQRankSum=-6;NLOD=15.79;ReadPosRankSum=1.9;TLOD=32.56;ANN=C|synonymous_variant|LOW|FAM231D|ENSG00000203815|transcript|ENST00000369173|protein_coding|1/1|c.195T>C|p.Ser65Ser|287/632|195/510|65/169||,C|upstream_gene_variant|MODIFIER|RNU1-68P|ENSG00000252925|transcript|ENST00000517116|snRNA||n.-4396A>G|||||4396|,C|intron_variant|MODIFIER|RP11-353N4.5|ENSG00000234232|transcript|ENST00000608683|lincRNA|2/2|n.378+24652A>G||||||,C|intron_variant|MODIFIER|RP11-353N4.4|ENSG00000223759|transcript|ENST00000443602|lincRNA|1/1|n.1447-482T>C|||||| GT:AD:AF:DP 0/1:198,23:0.102:221 0/0:115,6:0.045:121 | |
| chr1 150082790 . T C . t_lod_fstar ClippingRankSum=0;DP=69;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=1.077;TLOD=5.53;ANN=C|intron_variant|MODIFIER|VPS45|ENSG00000136631|transcript|ENST00000369130|protein_coding|14/14|c.1625+48T>C||||||,C|intron_variant|MODIFIER|VPS45|ENSG00000136631|transcript|ENST00000369128|protein_coding|12/13|c.1310+48T>C||||||,C|intron_variant|MODIFIER|VPS45|ENSG00000136631|transcript|ENST00000535106|protein_coding|13/13|c.*344+48T>C||||||,C|intron_variant|MODIFIER|VPS45|ENSG00000136631|transcript|ENST00000491789|processed_transcript|2/2|n.357+48T>C||||||,C|intron_variant|MODIFIER|VPS45|ENSG00000136631|transcript|ENST00000484306|processed_transcript|1/1|n.1454+48T>C|||||| GT:AD:AF:DP 0/1:41,4:0.088:45 0/0:24,0:0:24 | |
| chr1 150634240 . G T . t_lod_fstar ClippingRankSum=0;DP=98;ECNT=1;FS=2.212;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=1.425;TLOD=5.42;ANN=T|intron_variant|MODIFIER|GOLPH3L|ENSG00000143457|transcript|ENST00000271732|protein_coding|4/4|c.430+50C>A||||||,T|intron_variant|MODIFIER|GOLPH3L|ENSG00000143457|transcript|ENST00000540514|protein_coding|3/3|c.298+50C>A||||||,T|intron_variant|MODIFIER|GOLPH3L|ENSG00000143457|transcript|ENST00000427665|protein_coding|5/5|c.496+50C>A||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:61,4:0.065:65 0/0:33,0:0:33 | |
| chr1 151811483 . G T . t_lod_fstar ClippingRankSum=0;DP=111;ECNT=1;FS=0;HCNT=48;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.33;ReadPosRankSum=-0.103;TLOD=4.41;ANN=T|5_prime_UTR_variant|MODIFIER|C2CD4D|ENSG00000225556|transcript|ENST00000454109|protein_coding|2/2|c.-18C>A|||||18|,T|upstream_gene_variant|MODIFIER|AL450992.2|ENSG00000234614|transcript|ENST00000434182|antisense||n.-2870G>T|||||2870|,T|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000201134|transcript|ENST00000364264|misc_RNA||n.*2729C>A|||||2729| GT:AD:AF:DP 0/1:66,4:0.043:70 0/0:41,0:0:41 | |
| chr1 152187588 . C T . germline_risk ClippingRankSum=0;DP=274;ECNT=1;FS=4.644;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=34.58;MQ0=69;MQRankSum=1.07;NLOD=1.12;ReadPosRankSum=-3.211;TLOD=8.64;ANN=T|missense_variant|MODERATE|HRNR|ENSG00000197915|transcript|ENST00000368801|protein_coding|3/3|c.6517G>A|p.Gly2173Ser|6593/9623|6517/8553|2173/2850||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000593011|antisense|1/3|n.296+46692C>T||||||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000420707|antisense|1/8|n.158+25604C>T|||||| GT:AD:AF:DP 0/1:110,8:0.064:118 0/0:53,3:0.05:56 | |
| chr1 152188118 . C T . PASS ClippingRankSum=0;DP=515;ECNT=1;FS=3.831;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=45.19;MQ0=55;MQRankSum=0.658;NLOD=7.43;ReadPosRankSum=-1.347;TLOD=15.92;ANN=T|missense_variant|MODERATE|HRNR|ENSG00000197915|transcript|ENST00000368801|protein_coding|3/3|c.5987G>A|p.Arg1996His|6063/9623|5987/8553|1996/2850||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000593011|antisense|1/3|n.296+47222C>T||||||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000420707|antisense|1/8|n.158+26134C>T|||||| GT:AD:AF:DP 0/1:230,17:0.064:247 0/0:150,15:0.079:165 | |
| chr1 152287766 . C CTATCTTTGGTCTTGTCAGAGACTCTTACAAGACCAAAGATAGAGCA . t_lod_fstar ClippingRankSum=0;DP=174;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.82;ReadPosRankSum=-0.737;TLOD=5.04;ANN=CTATCTTTGGTCTTGTCAGAGACTCTTACAAGACCAAAGATAGAGCA|intron_variant|MODIFIER|FLG|ENSG00000143631|transcript|ENST00000368799|protein_coding|2/2|c.138+28_138+29insTGCTCTATCTTTGGTCTTGTAAGAGTCTCTGACAAGACCAAAGATA||||||,CTATCTTTGGTCTTGTCAGAGACTCTTACAAGACCAAAGATAGAGCA|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000392688|antisense|2/6|n.914+361_914+362insAAGACCAAAGATAGAGCATATCTTTGGTCTTGTCAGAGACTCTTAC||||||INFO_REALIGN_3_PRIME,CTATCTTTGGTCTTGTCAGAGACTCTTACAAGACCAAAGATAGAGCA|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000593011|antisense|3/3|n.428+361_428+362insAAGACCAAAGATAGAGCATATCTTTGGTCTTGTCAGAGACTCTTAC||||||INFO_REALIGN_3_PRIME,CTATCTTTGGTCTTGTCAGAGACTCTTACAAGACCAAAGATAGAGCA|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000420707|antisense|5/8|n.514+361_514+362insAAGACCAAAGATAGAGCATATCTTTGGTCTTGTCAGAGACTCTTAC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:96,1:0.029:97 0/0:62,0:0:62 | |
| chr1 152325429 . G T . t_lod_fstar ClippingRankSum=0;DP=141;ECNT=1;FS=2.079;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=59.58;MQ0=0;MQRankSum=0;NLOD=9.03;ReadPosRankSum=-0.355;TLOD=5.19;ANN=T|missense_variant|MODERATE|FLG2|ENSG00000143520|transcript|ENST00000388718|protein_coding|3/3|c.4833C>A|p.Phe1611Leu|4906/9124|4833/7176|1611/2391||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000392688|antisense|6/6|n.1407-11034G>T||||||,T|intron_variant|MODIFIER|FLG-AS1|ENSG00000237975|transcript|ENST00000445097|antisense|2/2|n.152-11034G>T|||||| GT:AD:AF:DP 0/1:90,3:0.051:93 0/0:46,0:0:46 | |
| chr1 152487959 . GCCT G . t_lod_fstar ClippingRankSum=0;DP=135;ECNT=1;FS=3.432;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.39;ReadPosRankSum=-0.383;TLOD=5.27;ANN=G|disruptive_inframe_deletion|MODERATE|CRCT1|ENSG00000169509|transcript|ENST00000368790|protein_coding|2/2|c.113_115delCCT|p.Ser38del|186/700|113/300|38/99||INFO_REALIGN_3_PRIME,G|downstream_gene_variant|MODIFIER|LCE5A|ENSG00000186207|transcript|ENST00000334269|protein_coding||c.*3593_*3595delCCT|||||3307| GT:AD:AF:DP 0/1:73,2:0.036:75 0/0:29,0:0:29 | |
| chr1 152883824 . C T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=17;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.20;ReadPosRankSum=-1.269;TLOD=4.32;ANN=T|synonymous_variant|LOW|IVL|ENSG00000163207|transcript|ENST00000368764|protein_coding|2/2|c.1551C>T|p.Asp517Asp|1615/2153|1551/1758|517/585||,T|synonymous_variant|LOW|IVL|ENSG00000163207|transcript|ENST00000392667|protein_coding|3/3|c.1113C>T|p.Asp371Asp|1479/2015|1113/1320|371/439|| GT:AD:AF:DP 0/1:11,2:0.167:13 0/0:4,0:0:4 | |
| chr1 153043332 . G A . germline_risk;t_lod_fstar ClippingRankSum=0;DP=44;ECNT=1;FS=3.188;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=38.65;MQ0=18;MQRankSum=-1.465;NLOD=1.81;ReadPosRankSum=-2.158;TLOD=4.90;ANN=A|splice_region_variant|LOW|SPRR2B|ENSG00000196805|transcript|ENST00000341611|protein_coding|2/2|c.-17C>T||||||,A|splice_region_variant|LOW|SPRR2B|ENSG00000196805|transcript|ENST00000368752|protein_coding|2/2|c.-17C>T||||||,A|5_prime_UTR_variant|MODIFIER|SPRR2B|ENSG00000196805|transcript|ENST00000341611|protein_coding|2/2|c.-17C>T|||||17|,A|5_prime_UTR_variant|MODIFIER|SPRR2B|ENSG00000196805|transcript|ENST00000368752|protein_coding|2/2|c.-17C>T|||||17|,A|upstream_gene_variant|MODIFIER|SPRR2B|ENSG00000196805|transcript|ENST00000368755|protein_coding||c.-17C>T|||||16| GT:AD:AF:DP 0/1:12,2:0.25:14 0/0:11,0:0:11 | |
| chr1 153066067 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=70;ECNT=2;FS=2.605;HCNT=6;MAX_ED=5;MIN_ED=5;MQ=59.3;MQ0=0;MQRankSum=-5.454;NLOD=1.22;ReadPosRankSum=-2.075;TLOD=7.75;ANN=T|missense_variant|MODERATE|SPRR2E|ENSG00000203785|transcript|ENST00000368750|protein_coding|2/2|c.161G>A|p.Cys54Tyr|222/678|161/219|54/72||,T|missense_variant|MODERATE|SPRR2E|ENSG00000203785|transcript|ENST00000368751|protein_coding|2/2|c.161G>A|p.Cys54Tyr|236/692|161/219|54/72||,T|intron_variant|MODIFIER|SPRR2B|ENSG00000196805|transcript|ENST00000368752|protein_coding|1/1|c.-19-22733G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:46,2:0.081:48:0|1:153066067_C_T 0/0:21,1:0.053:22:0|1:153066067_C_T | |
| chr1 153066072 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=74;ECNT=2;FS=5.18;HCNT=6;MAX_ED=5;MIN_ED=5;MQ=58.71;MQ0=0;MQRankSum=-5.176;NLOD=1.22;ReadPosRankSum=-2.116;TLOD=7.75;ANN=C|synonymous_variant|LOW|SPRR2E|ENSG00000203785|transcript|ENST00000368750|protein_coding|2/2|c.156A>G|p.Gln52Gln|217/678|156/219|52/72||,C|synonymous_variant|LOW|SPRR2E|ENSG00000203785|transcript|ENST00000368751|protein_coding|2/2|c.156A>G|p.Gln52Gln|231/692|156/219|52/72||,C|intron_variant|MODIFIER|SPRR2B|ENSG00000196805|transcript|ENST00000368752|protein_coding|1/1|c.-19-22738A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:48,3:0.081:51:0|1:153066067_C_T 0/0:22,1:0.053:23:0|1:153066067_C_T | |
| chr1 153606850 . GA G . t_lod_fstar ClippingRankSum=0;DP=144;ECNT=1;FS=1.836;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.05;ReadPosRankSum=0.156;TLOD=5.39;ANN=G|upstream_gene_variant|MODIFIER|RP1-178F15.5|ENSG00000271853|transcript|ENST00000497086|processed_transcript||n.-35delT|||||35|,G|upstream_gene_variant|MODIFIER|S100A13|ENSG00000189171|transcript|ENST00000368699|protein_coding||c.-7903delT|||||283|,G|upstream_gene_variant|MODIFIER|S100A13|ENSG00000189171|transcript|ENST00000491177|processed_transcript||n.-3015delT|||||3015|,G|upstream_gene_variant|MODIFIER|RP1-178F15.5|ENSG00000271853|transcript|ENST00000484413|processed_transcript||n.-326delT|||||326|,G|upstream_gene_variant|MODIFIER|RP1-178F15.5|ENSG00000271853|transcript|ENST00000472233|processed_transcript||n.-264delT|||||264|,G|upstream_gene_variant|MODIFIER|RP1-178F15.4|ENSG00000272030|transcript|ENST00000607839|antisense||n.-2178delT|||||2178|,G|upstream_gene_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000368690|protein_coding||c.-2214delA|||||2214|,G|upstream_gene_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000368687|protein_coding||c.-3930delA|||||3709|,G|upstream_gene_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000368686|protein_coding||c.-3975delA|||||3967|,G|downstream_gene_variant|MODIFIER|S100A1|ENSG00000160678|transcript|ENST00000368698|protein_coding||c.*2534delA|||||2341|,G|downstream_gene_variant|MODIFIER|S100A1|ENSG00000160678|transcript|ENST00000469893|processed_transcript||n.*2338delA|||||2338|,G|downstream_gene_variant|MODIFIER|S100A1|ENSG00000160678|transcript|ENST00000292169|protein_coding||c.*2534delA|||||2338|,G|downstream_gene_variant|MODIFIER|S100A1|ENSG00000160678|transcript|ENST00000368696|protein_coding||c.*2843delA|||||2571|,G|downstream_gene_variant|MODIFIER|S100A1|ENSG00000160678|transcript|ENST00000436839|protein_coding||c.*3750delA|||||3750|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000368694|protein_coding|1/5|c.-18+32delA||||||,G|intron_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000495554|processed_transcript|1/2|n.269+32delA||||||,G|intron_variant|MODIFIER|CHTOP|ENSG00000160679|transcript|ENST00000403433|protein_coding|1/4|c.-18+32delA||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP1-178F15.4|ENSG00000272030|transcript|ENST00000469931|antisense|1/5|n.23delT|||||| GT:AD:AF:DP 0/1:75,7:0.079:82 0/0:51,0:0:51 | |
| chr1 153634892 . TTTC T . PASS ClippingRankSum=0;DP=148;ECNT=1;FS=4.695;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.03;ReadPosRankSum=-0.038;TLOD=103.84;ANN=T|conservative_inframe_deletion|MODERATE|ILF2|ENSG00000143621|transcript|ENST00000361891|protein_coding|14/14|c.1150_1152delGAA|p.Glu384del|1278/1659|1150/1173|384/390||,T|downstream_gene_variant|MODIFIER|SNAPIN|ENSG00000143553|transcript|ENST00000368685|protein_coding||c.*1116_*1118delTTC|||||587|,T|downstream_gene_variant|MODIFIER|SNAPIN|ENSG00000143553|transcript|ENST00000474959|processed_transcript||n.*1167_*1169delTTC|||||1167|,T|downstream_gene_variant|MODIFIER|SNAPIN|ENSG00000143553|transcript|ENST00000462880|processed_transcript||n.*588_*590delTTC|||||588|,T|downstream_gene_variant|MODIFIER|SNAPIN|ENSG00000143553|transcript|ENST00000478558|processed_transcript||n.*853_*855delTTC|||||853|,T|downstream_gene_variant|MODIFIER|ILF2|ENSG00000143621|transcript|ENST00000368684|protein_coding||c.*3244_*3246delGAA|||||3246|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|ILF2|ENSG00000143621|transcript|ENST00000368681|protein_coding||c.*5077_*5079delGAA|||||4866|,T|non_coding_transcript_exon_variant|MODIFIER|ILF2|ENSG00000143621|transcript|ENST00000480213|processed_transcript|5/5|n.654_656delGAA|||||| GT:AD:AF:DP 0/1:48,37:0.458:85 0/0:57,0:0:57 | |
| chr1 154027185 . TGA T . t_lod_fstar ClippingRankSum=0;DP=103;ECNT=1;FS=0;HCNT=30;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.01;ReadPosRankSum=-0.266;TLOD=5.58;ANN=T|intron_variant|MODIFIER|NUP210L|ENSG00000143552|transcript|ENST00000368559|protein_coding|24/39|c.3303+59_3303+60delTC||||||,T|intron_variant|MODIFIER|NUP210L|ENSG00000143552|transcript|ENST00000368553|protein_coding|2/15|c.102+59_102+60delTC||||||,T|intron_variant|MODIFIER|NUP210L|ENSG00000143552|transcript|ENST00000271854|protein_coding|24/37|c.3303+59_3303+60delTC|||||| GT:AD:AF:DP 0/1:52,5:0.081:57 0/0:39,0:0:39 | |
| chr1 154294464 . A G . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=249;ECNT=3;FS=1.635;HCNT=18;MAX_ED=35;MIN_ED=7;MQ=47.35;MQ0=27;MQRankSum=-2.592;NLOD=0.647;ReadPosRankSum=-2.186;TLOD=40.38;ANN=G|missense_variant|MODERATE|AQP10|ENSG00000143595|transcript|ENST00000324978|protein_coding|2/6|c.161A>G|p.Asn54Ser|201/1791|161/906|54/301||,G|missense_variant|MODERATE|AQP10|ENSG00000143595|transcript|ENST00000484864|protein_coding|2/5|c.161A>G|p.Asn54Ser|197/2262|161/795|54/264||,G|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368487|protein_coding||c.-6154A>G|||||3565|,G|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368490|retained_intron||n.-3617A>G|||||3617|,G|intron_variant|MODIFIER|AQP10|ENSG00000143595|transcript|ENST00000355197|processed_transcript|1/3|n.171+728A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:126,21:0.127:147:0|1:154294464_A_G 0/0:66,7:0.077:73:0|1:154294464_A_G | |
| chr1 154294471 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=249;ECNT=3;FS=3.929;HCNT=18;MAX_ED=35;MIN_ED=7;MQ=47.77;MQ0=27;MQRankSum=-2.428;NLOD=0.948;ReadPosRankSum=-2.26;TLOD=42.94;ANN=T|synonymous_variant|LOW|AQP10|ENSG00000143595|transcript|ENST00000324978|protein_coding|2/6|c.168C>T|p.Phe56Phe|208/1791|168/906|56/301||,T|synonymous_variant|LOW|AQP10|ENSG00000143595|transcript|ENST00000484864|protein_coding|2/5|c.168C>T|p.Phe56Phe|204/2262|168/795|56/264||,T|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368487|protein_coding||c.-6147C>T|||||3558|,T|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368490|retained_intron||n.-3610C>T|||||3610|,T|intron_variant|MODIFIER|AQP10|ENSG00000143595|transcript|ENST00000355197|processed_transcript|1/3|n.171+735C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:126,18:0.137:144:0|1:154294464_A_G 0/0:69,7:0.075:76:0|1:154294464_A_G | |
| chr1 154294499 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=212;ECNT=3;FS=13.328;HCNT=17;MAX_ED=35;MIN_ED=7;MQ=49.3;MQ0=27;MQRankSum=-1.535;NLOD=4.00;ReadPosRankSum=-1.931;TLOD=8.34;ANN=A|missense_variant|MODERATE|AQP10|ENSG00000143595|transcript|ENST00000324978|protein_coding|2/6|c.196G>A|p.Val66Ile|236/1791|196/906|66/301||,A|missense_variant|MODERATE|AQP10|ENSG00000143595|transcript|ENST00000484864|protein_coding|2/5|c.196G>A|p.Val66Ile|232/2262|196/795|66/264||,A|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368487|protein_coding||c.-6119G>A|||||3530|,A|upstream_gene_variant|MODIFIER|ATP8B2|ENSG00000143515|transcript|ENST00000368490|retained_intron||n.-3582G>A|||||3582|,A|intron_variant|MODIFIER|AQP10|ENSG00000143595|transcript|ENST00000355197|processed_transcript|1/3|n.171+763G>A|||||| GT:AD:AF:DP 0/1:106,6:0.071:112 0/0:67,4:0.077:71 | |
| chr1 154523891 . C T . t_lod_fstar ClippingRankSum=0;DP=73;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=-0.898;TLOD=4.58;ANN=T|synonymous_variant|LOW|UBE2Q1|ENSG00000160714|transcript|ENST00000292211|protein_coding|11/13|c.1152G>A|p.Val384Val|1232/3210|1152/1269|384/422||,T|upstream_gene_variant|MODIFIER|UBE2Q1-AS1|ENSG00000229780|transcript|ENST00000441613|antisense||n.-2194C>T|||||2194|,T|downstream_gene_variant|MODIFIER|TDRD10|ENSG00000163239|transcript|ENST00000368480|protein_coding||c.*3858C>T|||||3268|,T|downstream_gene_variant|MODIFIER|TDRD10|ENSG00000163239|transcript|ENST00000368482|protein_coding||c.*3705C>T|||||3268|,T|downstream_gene_variant|MODIFIER|TDRD10|ENSG00000163239|transcript|ENST00000479937|processed_transcript||n.*3268C>T|||||3268|,T|downstream_gene_variant|MODIFIER|TDRD10|ENSG00000163239|transcript|ENST00000468714|processed_transcript||n.*3936C>T|||||3936|,T|downstream_gene_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000483639|processed_transcript||n.*45G>A|||||45|,T|downstream_gene_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000474181|processed_transcript||n.*336G>A|||||336|,T|downstream_gene_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000497453|processed_transcript||n.*967G>A|||||967|,T|non_coding_transcript_exon_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000467683|processed_transcript|3/5|n.224G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000491572|processed_transcript|2/3|n.165G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|UBE2Q1|ENSG00000160714|transcript|ENST00000476612|processed_transcript|2/2|n.109G>A|||||| GT:AD:AF:DP 0/1:37,4:0.074:41 0/0:32,0:0:32 | |
| chr1 154917507 . CGGT C . t_lod_fstar ClippingRankSum=0;DP=78;ECNT=1;FS=1.935;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.71;ReadPosRankSum=0.649;TLOD=5.94;ANN=C|disruptive_inframe_deletion|MODERATE|PBXIP1|ENSG00000163346|transcript|ENST00000368463|protein_coding|11/11|c.2186_2188delACC|p.His729del|2260/3212|2186/2196|729/731||,C|disruptive_inframe_deletion|MODERATE|PBXIP1|ENSG00000163346|transcript|ENST00000368465|protein_coding|10/10|c.2099_2101delACC|p.His700del|2188/3144|2099/2109|700/702||,C|disruptive_inframe_deletion|MODERATE|PBXIP1|ENSG00000163346|transcript|ENST00000539880|protein_coding|8/8|c.1667_1669delACC|p.His556del|1744/2191|1667/1677|556/558||,C|disruptive_inframe_deletion|MODERATE|PBXIP1|ENSG00000163346|transcript|ENST00000542459|protein_coding|8/8|c.1721_1723delACC|p.His574del|1843/1865|1721/1731|574/576||,C|downstream_gene_variant|MODIFIER|PBXIP1|ENSG00000163346|transcript|ENST00000368460|protein_coding||c.*2212_*2214delACC|||||2066|,C|downstream_gene_variant|MODIFIER|PBXIP1|ENSG00000163346|transcript|ENST00000498553|processed_transcript||n.*2385_*2387delACC|||||2387|,C|downstream_gene_variant|MODIFIER|PBXIP1|ENSG00000163346|transcript|ENST00000490230|nonsense_mediated_decay||c.*3333_*3335delACC|||||2621| GT:AD:AF:DP 0/1:34,4:0.077:38 0/0:26,0:0:26 | |
| chr1 155796840 . G T . t_lod_fstar ClippingRankSum=0;DP=53;ECNT=1;FS=2.653;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.91;ReadPosRankSum=0;TLOD=4.13;ANN=T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000368331|protein_coding|2/31|c.506-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000437809|protein_coding|2/31|c.506-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000271883|protein_coding|2/31|c.506-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000361040|protein_coding|2/20|c.506-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000471341|processed_transcript|2/19|n.603-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000468867|processed_transcript|2/3|n.250-21C>A||||||,T|intron_variant|MODIFIER|GON4L|ENSG00000116580|transcript|ENST00000488251|processed_transcript|2/2|n.621-21C>A|||||| GT:AD:AF:DP 0/1:31,2:0.08:33 0/0:20,0:0:20 | |
| chr1 156263011 . CAG C . t_lod_fstar ClippingRankSum=0;DP=64;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.90;ReadPosRankSum=0.733;TLOD=4.31;ANN=C|upstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000497831|processed_transcript||n.-1672_-1671delCT|||||1671|,C|upstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000480968|processed_transcript||n.-1716_-1715delCT|||||1715|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000295694|protein_coding||c.*1623_*1624delAG|||||778|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000463670|processed_transcript||n.*778_*779delAG|||||778|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000357501|protein_coding||c.*1564_*1565delAG|||||1273|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000405535|protein_coding||c.*1623_*1624delAG|||||778|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000495881|processed_transcript||n.*778_*779delAG|||||778|,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000456810|protein_coding||c.*1696_*1697delAG|||||1696|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|TMEM79|ENSG00000163472|transcript|ENST00000485135|processed_transcript||n.*36_*37delAG|||||36|,C|downstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000476177|nonsense_mediated_decay||c.*1237_*1238delCT|||||152|,C|downstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000497955|retained_intron||n.*162_*163delCT|||||163|,C|downstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000368264|nonsense_mediated_decay||c.*477_*478delCT|||||202|,C|downstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000479084|retained_intron||n.*296_*297delCT|||||297|,C|downstream_gene_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000484214|retained_intron||n.*395_*396delCT|||||396|,C|intron_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000362007|protein_coding|5/5|c.1056-13_1056-12delCT||||||,C|intron_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000461597|nonsense_mediated_decay|1/2|c.63-13_63-12delCT||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000472870|nonsense_mediated_decay|2/3|c.379-102_379-101delCT||||||,C|intron_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000482579|processed_transcript|1/1|n.51-13_51-12delCT||||||,C|intron_variant|MODIFIER|C1orf85|ENSG00000198715|transcript|ENST00000481050|protein_coding|2/2|c.168-13_168-12delCT||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:36,3:0.069:39 0/0:19,0:0:19 | |
| chr1 156453109 . C T . PASS ClippingRankSum=0;DP=25;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.40;ReadPosRankSum=-1.102;TLOD=21.59;ANN=T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000348159|protein_coding|2/12|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000464356|protein_coding|1/10|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000340875|protein_coding|2/12|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000353795|protein_coding|2/11|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000368240|protein_coding|2/11|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000360595|protein_coding|2/11|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000475587|nonsense_mediated_decay|2/9|c.-25G>A|||||25|,T|5_prime_UTR_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000489057|protein_coding|3/3|c.-25G>A|||||25|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|MEF2D|ENSG00000116604|transcript|ENST00000493077|retained_intron||n.-3537G>A|||||3537|,T|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000206651|transcript|ENST00000383924|misc_RNA||n.*781G>A|||||781| GT:AD:AF:DP 0/1:5,9:0.7:14 0/0:11,0:0:11 | |
| chr1 156894385 . T C . t_lod_fstar ClippingRankSum=0;DP=133;ECNT=1;FS=26.37;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=59.78;MQ0=0;MQRankSum=0;NLOD=6.64;ReadPosRankSum=-3.336;TLOD=4.97;ANN=C|upstream_gene_variant|MODIFIER|LRRC71|ENSG00000160838|transcript|ENST00000476550|processed_transcript||n.-2769T>C|||||2769|,C|intron_variant|MODIFIER|LRRC71|ENSG00000160838|transcript|ENST00000337428|protein_coding|3/14|c.439+41T>C||||||,C|intron_variant|MODIFIER|LRRC71|ENSG00000160838|transcript|ENST00000490146|processed_transcript|4/15|n.419+41T>C|||||| GT:AD:AF:DP 0/1:84,4:0.037:88 0/0:35,1:0.027:36 | |
| chr1 158389958 . A G . t_lod_fstar ClippingRankSum=0;DP=107;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=-0.92;TLOD=4.02;ANN=G|synonymous_variant|LOW|OR10K2|ENSG00000180708|transcript|ENST00000314902|protein_coding|1/1|c.699T>C|p.Gly233Gly|699/939|699/939|233/312|| GT:AD:AF:DP 0/1:72,2:0.035:74 0/0:33,0:0:33 | |
| chr1 159035759 . T A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=243;ECNT=8;FS=2.989;HCNT=4;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.75;ReadPosRankSum=-1.435;TLOD=4.48;ANN=A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.757A>T|p.Asn253Tyr|1046/1529|757/1032|253/343||,A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.346A>T|p.Asn116Tyr|439/594|346/501|116/166||WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*347A>T|||||347|,A|non_coding_transcript_exon_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.306A>T|||||| GT:AD:AF:DP:PGT:PID 0/1:175,2:0.015:177:0|1:159035759_T_A 0/0:66,0:0:66:0|1:159035759_T_A | |
| chr1 159035765 . T A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=262;ECNT=8;FS=12.083;HCNT=13;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.31;ReadPosRankSum=-1.296;TLOD=4.48;ANN=A|stop_gained|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.751A>T|p.Lys251*|1040/1529|751/1032|251/343||,A|stop_gained|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.340A>T|p.Lys114*|433/594|340/501|114/166||WARNING_TRANSCRIPT_NO_STOP_CODON,A|structural_interaction_variant|HIGH|AIM2|ENSG00000163568|interaction|3RN5:A_251-A_287:ENST00000368130|protein_coding|4/6|c.751A>T||||||,A|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*341A>T|||||341|,A|non_coding_transcript_exon_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.300A>T||||||;LOF=(AIM2|ENSG00000163568|4|0.50);NMD=(AIM2|ENSG00000163568|4|0.50) GT:AD:AF:DP 0/1:186,2:0.015:188 0/0:69,3:0.059:72 | |
| chr1 159035768 . G T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=262;ECNT=8;FS=21.194;HCNT=30;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.90;ReadPosRankSum=-0.762;TLOD=4.52;ANN=T|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.748C>A|p.Pro250Thr|1037/1529|748/1032|250/343||,T|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.337C>A|p.Pro113Thr|430/594|337/501|113/166||WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*338C>A|||||338|,T|non_coding_transcript_exon_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.297C>A|||||| GT:AD:AF:DP 0/1:186,2:0.015:188 0/0:66,6:0.122:72 | |
| chr1 159035772 . T A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=264;ECNT=8;FS=3.018;HCNT=4;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.05;ReadPosRankSum=-0.507;TLOD=4.47;ANN=A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.744A>T|p.Glu248Asp|1033/1529|744/1032|248/343||,A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.333A>T|p.Glu111Asp|426/594|333/501|111/166||WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*334A>T|||||334|,A|non_coding_transcript_exon_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.293A>T|||||| GT:AD:AF:DP:PGT:PID 0/1:190,2:0.015:192:0|1:159035759_T_A 0/0:72,0:0:72:0|1:159035759_T_A | |
| chr1 159035777 . C A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=272;ECNT=8;FS=43.593;HCNT=19;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.45;ReadPosRankSum=-0.236;TLOD=4.30;ANN=A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.739G>T|p.Gly247Cys|1028/1529|739/1032|247/343||,A|missense_variant|MODERATE|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.328G>T|p.Gly110Cys|421/594|328/501|110/166||WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*329G>T|||||329|,A|non_coding_transcript_exon_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.288G>T|||||| GT:AD:AF:DP 0/1:184,10:0.053:194 0/0:72,5:0.096:77 | |
| chr1 159035778 . AGCTTT A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=284;ECNT=8;FS=3.024;HCNT=4;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.16;ReadPosRankSum=-0.091;TLOD=4.37;ANN=A|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.733_737delAAAGC|p.Lys245fs|1026/1529|733/1032|245/343||,A|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.322_326delAAAGC|p.Lys108fs|419/594|322/501|108/166||WARNING_TRANSCRIPT_NO_STOP_CODON,A|splice_region_variant&non_coding_transcript_exon_variant|LOW|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|4/5|n.282_286delAAAGC||||||,A|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*323_*327delAAAGC|||||327|;LOF=(AIM2|ENSG00000163568|4|0.50) GT:AD:AF:DP:PGT:PID 0/1:203,2:0.013:205:0|1:159035759_T_A 0/0:79,0:0:79:0|1:159035759_T_A | |
| chr1 159035785 . CTG C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=284;ECNT=8;FS=3.024;HCNT=4;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=16.25;TLOD=4.41;ANN=C|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.729_730delCA|p.Ile243fs|1019/1529|729/1032|243/343||,C|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.318_319delCA|p.Ile106fs|412/594|318/501|106/166||WARNING_TRANSCRIPT_NO_STOP_CODON,C|splice_acceptor_variant&splice_region_variant&intron_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|3/4|n.281-3_281-2delCA||||||,C|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*319_*320delCA|||||320|;LOF=(AIM2|ENSG00000163568|4|0.50) GT:AD:AF:DP:PGT:PID 0/1:203,2:0.014:205:0|1:159035759_T_A 0/0:79,0:0:79:0|1:159035759_T_A | |
| chr1 159035789 . T TTAAAAAA . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=283;ECNT=8;FS=3.025;HCNT=4;MAX_ED=30;MIN_ED=6;MQ=60;MQ0=0;MQRankSum=0;NLOD=16.25;TLOD=4.46;ANN=TTAAAAAA|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368130|protein_coding|4/6|c.726_727insTTTTTTA|p.Ile243fs|1015/1529|726/1032|242/343||,TTAAAAAA|frameshift_variant|HIGH|AIM2|ENSG00000163568|transcript|ENST00000368129|protein_coding|2/3|c.315_316insTTTTTTA|p.Ile106fs|408/594|315/501|105/166||WARNING_TRANSCRIPT_NO_STOP_CODON,TTAAAAAA|splice_region_variant&intron_variant|LOW|AIM2|ENSG00000163568|transcript|ENST00000481829|processed_transcript|3/4|n.281-6_281-5insTTTTTTA||||||,TTAAAAAA|downstream_gene_variant|MODIFIER|AIM2|ENSG00000163568|transcript|ENST00000411768|processed_transcript||n.*316_*317insTTTTTTA|||||316|;LOF=(AIM2|ENSG00000163568|4|0.50) GT:AD:AF:DP:PGT:PID 0/1:203,2:0.014:205:0|1:159035759_T_A 0/0:78,0:0:78:0|1:159035759_T_A | |
| chr1 160054229 . GTGC G . t_lod_fstar ClippingRankSum=0;DP=157;ECNT=1;FS=2.638;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.92;ReadPosRankSum=0.386;TLOD=5.26;ANN=G|disruptive_inframe_deletion|MODERATE|KCNJ9|ENSG00000162728|transcript|ENST00000368088|protein_coding|2/3|c.422_424delTGC|p.Leu141del|664/4170|422/1182|141/393||INFO_REALIGN_3_PRIME,G|downstream_gene_variant|MODIFIER|RP11-536C5.2|ENSG00000225279|transcript|ENST00000435580|antisense||n.*4619_*4621delTGC|||||4619| GT:AD:AF:DP 0/1:76,2:0.036:78 0/0:44,0:0:44 | |
| chr1 161576331 . C T . t_lod_fstar ClippingRankSum=0;DP=220;ECNT=1;FS=4.456;HCNT=15;MAX_ED=.;MIN_ED=.;MQ=45.68;MQ0=24;MQRankSum=-2.098;NLOD=13.23;ReadPosRankSum=-0.24;TLOD=4.08;ANN=T|downstream_gene_variant|MODIFIER|RP11-25K21.6|ENSG00000273112|transcript|ENST00000537821|processed_transcript||n.*1442C>T|||||1442|,T|downstream_gene_variant|MODIFIER|FCGR2C|ENSG00000244682|transcript|ENST00000467903|processed_transcript||n.*879C>T|||||879|,T|downstream_gene_variant|MODIFIER|FCGR2C|ENSG00000244682|transcript|ENST00000507374|processed_transcript||n.*1442C>T|||||1442|,T|downstream_gene_variant|MODIFIER|FCGR2C|ENSG00000244682|transcript|ENST00000508651|processed_transcript||n.*1404C>T|||||1404|,T|intron_variant|MODIFIER|FCGR3A|ENSG00000203747|transcript|ENST00000540048|protein_coding|2/4|c.61+23827G>A||||||,T|intron_variant|MODIFIER|FCGR2B|ENSG00000072694|transcript|ENST00000367960|protein_coding|1/6|c.112+24992C>T||||||,T|intron_variant|MODIFIER|FCGR2B|ENSG00000072694|transcript|ENST00000367962|protein_coding|2/7|c.133+18099C>T||||||,T|intron_variant|MODIFIER|FCGR2B|ENSG00000072694|transcript|ENST00000403078|protein_coding|2/6|c.133+18099C>T||||||,T|intron_variant|MODIFIER|FCGR2B|ENSG00000072694|transcript|ENST00000428605|protein_coding|2/5|c.133+18099C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|HSPA7|ENSG00000225217|transcript|ENST00000445535|unprocessed_pseudogene|1/1|n.251C>T|||||| GT:AD:AF:DP 0/1:115,4:0.037:119 0/0:74,0:0:74 | |
| chr1 162773336 . AAT A . t_lod_fstar ClippingRankSum=0;DP=271;ECNT=1;FS=1.693;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=59.45;MQ0=2;MQRankSum=-3.237;NLOD=15.05;ReadPosRankSum=-3.414;TLOD=5.88;ANN=A|downstream_gene_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000463037|processed_transcript||n.*3610_*3611delAT|||||3610|,A|downstream_gene_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000466176|nonsense_mediated_decay||c.*6915_*6916delAT|||||3713|,A|downstream_gene_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000484251|processed_transcript||n.*3610_*3611delAT|||||3610|,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000254521|protein_coding|6/8|c.747+15_747+16delTA||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000485405|processed_transcript|6/8|n.1865+15_1865+16delTA||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000367917|protein_coding|5/7|c.643-717_643-716delTA||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000494450|retained_intron|2/2|n.539+15_539+16delTA||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000470195|nonsense_mediated_decay|2/4|c.*22-717_*22-716delTA||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HSD17B7|ENSG00000132196|transcript|ENST00000488656|retained_intron|1/1|n.618+15_618+16delTA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:184,5:0.024:189 0/0:76,0:0:76 | |
| chr1 167849640 . CTTCT C . PASS ClippingRankSum=0;DP=113;ECNT=1;FS=0;HCNT=40;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.73;ReadPosRankSum=-0.319;TLOD=46.06;ANN=C|intron_variant|MODIFIER|ADCY10|ENSG00000143199|transcript|ENST00000367851|protein_coding|10/32|c.1139+85_1139+88delAGAA||||||,C|intron_variant|MODIFIER|ADCY10|ENSG00000143199|transcript|ENST00000545172|protein_coding|7/29|c.680+85_680+88delAGAA||||||,C|intron_variant|MODIFIER|ADCY10|ENSG00000143199|transcript|ENST00000367848|protein_coding|10/32|c.863+85_863+88delAGAA|||||| GT:AD:AF:DP 0/1:56,18:0.26:74 0/0:37,0:0:37 | |
| chr1 171254351 . T A . t_lod_fstar ClippingRankSum=0;DP=50;ECNT=1;FS=10.669;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.01;ReadPosRankSum=1.268;TLOD=4.03;ANN=A|missense_variant|MODERATE|FMO1|ENSG00000010932|transcript|ENST00000354841|protein_coding|8/8|c.1267T>A|p.Cys423Ser|1398/2160|1267/1599|423/532||,A|missense_variant|MODERATE|FMO1|ENSG00000010932|transcript|ENST00000367750|protein_coding|9/9|c.1267T>A|p.Cys423Ser|1389/2155|1267/1599|423/532||,A|missense_variant|MODERATE|FMO1|ENSG00000010932|transcript|ENST00000402921|protein_coding|8/8|c.1078T>A|p.Cys360Ser|1157/1572|1078/1410|360/469||,A|downstream_gene_variant|MODIFIER|FMO1|ENSG00000010932|transcript|ENST00000472893|processed_transcript||n.*2016T>A|||||2016|,A|non_coding_transcript_exon_variant|MODIFIER|FMO1|ENSG00000010932|transcript|ENST00000469112|processed_transcript|9/9|n.2365T>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|FMO1|ENSG00000010932|transcript|ENST00000469711|processed_transcript|2/2|n.87T>A|||||| GT:AD:AF:DP 0/1:36,2:0.071:38 0/0:12,0:0:12 | |
| chr1 171483739 . G T . t_lod_fstar ClippingRankSum=0;DP=335;ECNT=1;FS=4.44;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.51;ReadPosRankSum=0.065;TLOD=4.39;ANN=T|missense_variant|MODERATE|PRRC2C|ENSG00000117523|transcript|ENST00000392078|protein_coding|4/35|c.355G>T|p.Ala119Ser|636/8978|355/8697|119/2898||,T|missense_variant|MODERATE|PRRC2C|ENSG00000117523|transcript|ENST00000426496|protein_coding|4/32|c.349G>T|p.Ala117Ser|630/8540|349/8259|117/2752||,T|missense_variant|MODERATE|PRRC2C|ENSG00000117523|transcript|ENST00000367742|protein_coding|4/34|c.355G>T|p.Ala119Ser|597/10366|355/8460|119/2819||,T|missense_variant|MODERATE|PRRC2C|ENSG00000117523|transcript|ENST00000338920|protein_coding|4/34|c.349G>T|p.Ala117Ser|586/10355|349/8454|117/2817||,T|non_coding_transcript_exon_variant|MODIFIER|PRRC2C|ENSG00000117523|transcript|ENST00000476522|processed_transcript|4/12|n.597G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|PRRC2C|ENSG00000117523|transcript|ENST00000467601|processed_transcript|4/5|n.546G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|PRRC2C|ENSG00000117523|transcript|ENST00000463586|retained_intron|2/3|n.3678G>T|||||| GT:AD:AF:DP 0/1:233,4:0.019:237 0/0:98,0:0:98 | |
| chr1 172412924 . C T . t_lod_fstar ClippingRankSum=0;DP=168;ECNT=1;FS=5.129;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.04;ReadPosRankSum=1.341;TLOD=4.56;ANN=T|5_prime_UTR_variant|MODIFIER|PIGC|ENSG00000135845|transcript|ENST00000367728|protein_coding|1/1|c.-1162G>A|||||1162|,T|upstream_gene_variant|MODIFIER|C1orf105|ENSG00000180999|transcript|ENST00000488100|protein_coding||c.-1355C>T|||||1355|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|C1orf105|ENSG00000180999|transcript|ENST00000367727|protein_coding|1/6|c.22-1289C>T||||||,T|intron_variant|MODIFIER|PIGC|ENSG00000135845|transcript|ENST00000258324|protein_coding|1/1|c.-232+204G>A||||||,T|intron_variant|MODIFIER|PIGC|ENSG00000135845|transcript|ENST00000484368|processed_transcript|1/4|n.96+204G>A||||||,T|intron_variant|MODIFIER|PIGC|ENSG00000135845|transcript|ENST00000344529|protein_coding|1/1|c.-209+204G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|PIGC|ENSG00000135845|transcript|ENST00000478184|processed_transcript|1/2|n.163G>A|||||| GT:AD:AF:DP 0/1:91,4:0.037:95 0/0:70,0:0:70 | |
| chr1 173795821 . A T . PASS ClippingRankSum=0;DP=76;ECNT=1;FS=17.53;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60.09;MQ0=0;MQRankSum=0.401;NLOD=4.21;ReadPosRankSum=0.717;TLOD=10.80;ANN=T|splice_region_variant&intron_variant|LOW|DARS2|ENSG00000117593|transcript|ENST00000361951|protein_coding|1/16|c.128-4A>T||||||,T|splice_region_variant&intron_variant|LOW|DARS2|ENSG00000117593|transcript|ENST00000239457|protein_coding|1/15|c.-1127-4A>T||||||,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000356198|protein_coding||c.-15384T>A|||||2361|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000345664|protein_coding||c.-15384T>A|||||2551|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000367710|protein_coding||c.-15384T>A|||||2509|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000496683|processed_transcript||n.-2552T>A|||||2552|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000460816|processed_transcript||n.-2348T>A|||||2348|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000484920|processed_transcript||n.-2664T>A|||||2664|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000479159|processed_transcript||n.-1963T>A|||||1963|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000493233|processed_transcript||n.-2538T>A|||||2538|,T|upstream_gene_variant|MODIFIER|CENPL|ENSG00000120334|transcript|ENST00000495275|processed_transcript||n.-2210T>A|||||2210| GT:AD:AF:DP 0/1:49,8:0.151:57 0/0:14,0:0:14 | |
| chr1 175086061 . AT A . PASS ClippingRankSum=0;DP=87;ECNT=1;FS=3.281;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.68;ReadPosRankSum=0.614;TLOD=15.57;ANN=A|splice_region_variant&intron_variant|LOW|TNN|ENSG00000120332|transcript|ENST00000239462|protein_coding|9/18|c.2120-4delT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:27,26:0.5:53 0/0:29,2:0:31 | |
| chr1 181686330 . G A . PASS ClippingRankSum=0;DP=108;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=-1.151;TLOD=51.13;ANN=A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000367573|protein_coding|11/48|c.1417G>A|p.Val473Ile|1417/7067|1417/6942|473/2313||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000357570|protein_coding|11/48|c.1270G>A|p.Val424Ile|1582/9848|1270/6795|424/2264||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000358338|protein_coding|11/46|c.1270G>A|p.Val424Ile|1582/9662|1270/6609|424/2202||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000367567|protein_coding|11/47|c.238G>A|p.Val80Ile|1582/9719|238/5634|80/1877||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000367570|protein_coding|11/47|c.1417G>A|p.Val473Ile|1582/9724|1417/6813|473/2270||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000526775|protein_coding|11/46|c.1417G>A|p.Val473Ile|1582/16170|1417/6756|473/2251||,A|missense_variant|MODERATE|CACNA1E|ENSG00000198216|transcript|ENST00000360108|protein_coding|11/47|c.1417G>A|p.Val473Ile|1424/6970|1417/6885|473/2294||,A|downstream_gene_variant|MODIFIER|CACNA1E|ENSG00000198216|transcript|ENST00000524607|protein_coding||c.*1065G>A|||||1065|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:54,29:0.37:83 0/0:25,0:0:25 | |
| chr1 182922000 . TCCGCCG T . germline_risk;t_lod_fstar ClippingRankSum=0;DP=60;ECNT=1;FS=0;HCNT=34;MAX_ED=.;MIN_ED=.;MQ=60.18;MQ0=0;MQRankSum=0;NLOD=1.18;ReadPosRankSum=-0.253;TLOD=4.93;ANN=T|disruptive_inframe_deletion|MODERATE|SHCBP1L|ENSG00000157060|transcript|ENST00000367547|protein_coding|1/10|c.263_268delCGGCGG|p.Ala88_Ala89del|505/2317|263/1962|88/653||,T|upstream_gene_variant|MODIFIER|SHCBP1L|ENSG00000157060|transcript|ENST00000423786|protein_coding||c.-887_-882delCGGCGG|||||882|,T|upstream_gene_variant|MODIFIER|SHCBP1L|ENSG00000157060|transcript|ENST00000467208|processed_transcript||n.-122_-117delCGGCGG|||||117|,T|downstream_gene_variant|MODIFIER|RP11-505O17.1|ENSG00000226570|transcript|ENST00000418657|processed_pseudogene||n.*2519_*2524delCGGCGG|||||2524|,T|non_coding_transcript_exon_variant|MODIFIER|SHCBP1L|ENSG00000157060|transcript|ENST00000483655|processed_transcript|1/11|n.153_158delCGGCGG||||||,T|non_coding_transcript_exon_variant|MODIFIER|SHCBP1L|ENSG00000157060|transcript|ENST00000488956|processed_transcript|1/9|n.655_660delCGGCGG||||||,T|non_coding_transcript_exon_variant|MODIFIER|SHCBP1L|ENSG00000157060|transcript|ENST00000497549|processed_transcript|1/4|n.241_246delCGGCGG|||||| GT:AD:AF:DP 0/1:21,2:0.167:23 0/0:5,0:0:5 | |
| chr1 184039831 . G T . t_lod_fstar ClippingRankSum=0;DP=215;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.53;ReadPosRankSum=-2.887;TLOD=4.70;ANN=T|3_prime_UTR_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000462677|nonsense_mediated_decay|4/6|c.*21G>T|||||21|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000361641|protein_coding|3/4|c.354-1460G>T||||||,T|intron_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000485209|nonsense_mediated_decay|4/5|c.*74-1460G>T||||||,T|intron_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000533373|protein_coding|3/4|c.354-1460G>T||||||,T|intron_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000423085|protein_coding|3/3|c.354-2130G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|TSEN15|ENSG00000198860|transcript|ENST00000367518|retained_intron|4/4|n.458G>T|||||| GT:AD:AF:DP 0/1:156,5:0.028:161 0/0:54,0:0:54 | |
| chr1 185137460 . TA T . t_lod_fstar ClippingRankSum=0;DP=407;ECNT=1;FS=2.489;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.10;ReadPosRankSum=1.633;TLOD=4.14;ANN=T|downstream_gene_variant|MODIFIER|CTA-253N17.1|ENSG00000231084|transcript|ENST00000413694|processed_pseudogene||n.*3006delT|||||3006|,T|intron_variant|MODIFIER|SWT1|ENSG00000116668|transcript|ENST00000367500|protein_coding|3/18|c.166-11delA||||||,T|intron_variant|MODIFIER|SWT1|ENSG00000116668|transcript|ENST00000367501|protein_coding|3/18|c.166-11delA||||||,T|intron_variant|MODIFIER|SWT1|ENSG00000116668|transcript|ENST00000450350|protein_coding|3/4|c.166-11delA||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:243,23:0.087:266 0/0:114,6:0.057:120 | |
| chr1 185897720 . G T . t_lod_fstar ClippingRankSum=0;DP=341;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=20.76;ReadPosRankSum=2.157;TLOD=4.04;ANN=T|missense_variant|MODERATE|HMCN1|ENSG00000143341|transcript|ENST00000271588|protein_coding|10/107|c.1473G>T|p.Leu491Phe|1702/18208|1473/16908|491/5635||,T|missense_variant|MODERATE|HMCN1|ENSG00000143341|transcript|ENST00000367492|protein_coding|10/106|c.1473G>T|p.Leu491Phe|1702/17861|1473/16557|491/5518|| GT:AD:AF:DP 0/1:234,4:0.018:238 0/0:100,0:0:100 | |
| chr1 186295329 . TTCA T . t_lod_fstar ClippingRankSum=0;DP=135;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.50;ReadPosRankSum=1.892;TLOD=5.29;ANN=T|disruptive_inframe_deletion|MODERATE|TPR|ENSG00000047410|transcript|ENST00000367478|protein_coding|41/51|c.5925_5927delTGA|p.Asp1975del|6224/9708|5925/7092|1975/2363||,T|upstream_gene_variant|MODIFIER|TPR|ENSG00000047410|transcript|ENST00000467810|processed_transcript||n.-3499_-3497delTGA|||||3497|,T|non_coding_transcript_exon_variant|MODIFIER|TPR|ENSG00000047410|transcript|ENST00000492973|retained_intron|1/2|n.21_23delTGA|||||| GT:AD:AF:DP 0/1:78,3:0.037:81 0/0:32,0:0:32 | |
| chr1 186300613 . G T . t_lod_fstar ClippingRankSum=0;DP=239;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=16.55;ReadPosRankSum=-0.325;TLOD=4.32;ANN=T|intron_variant|MODIFIER|TPR|ENSG00000047410|transcript|ENST00000367478|protein_coding|39/50|c.5688+17C>A|||||| GT:AD:AF:DP 0/1:156,5:0.026:161 0/0:77,0:0:77 | |
| chr1 193020842 . GTA G . t_lod_fstar ClippingRankSum=0;DP=496;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.88;ReadPosRankSum=1.682;TLOD=4.29;ANN=G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin)|ENST00000367455|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|modified-residue:N6-succinyllysine|ENST00000367455|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin)|ENST00000367454|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|modified-residue:N6-succinyllysine|ENST00000367454|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin)|ENST00000367448|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|modified-residue:N6-succinyllysine|ENST00000367448|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin)|ENST00000367449|protein_coding||c.140+40_140+41delTA||||||,G|sequence_feature|MODERATE|UCHL5|ENSG00000116750|modified-residue:N6-succinyllysine|ENST00000367449|protein_coding||c.140+40_140+41delTA||||||,G|downstream_gene_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000417752|protein_coding||c.*78_*79delTA|||||79|WARNING_TRANSCRIPT_NO_STOP_CODON,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367450|protein_coding|2/11|c.176+40_176+41delTA||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367455|protein_coding|2/10|c.140+40_140+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367454|protein_coding|2/10|c.140+40_140+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367451|protein_coding|2/11|c.140+40_140+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367448|protein_coding|2/11|c.140+40_140+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367449|protein_coding|2/10|c.140+40_140+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000367452|protein_coding|2/10|c.-233+40_-233+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000530098|protein_coding|2/9|c.-127+40_-127+41delTA||||||,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000421683|protein_coding|2/8|c.113+40_113+41delTA||||||WARNING_TRANSCRIPT_NO_STOP_CODON,G|intron_variant|MODIFIER|UCHL5|ENSG00000116750|transcript|ENST00000483156|processed_transcript|2/2|n.97+40_97+41delTA|||||| GT:AD:AF:DP 0/1:337,4:0.013:341 0/0:138,6:0.041:144 | |
| chr1 193181480 . CTAA C . PASS ClippingRankSum=0;DP=596;ECNT=1;FS=2.656;HCNT=52;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=1.997;NLOD=34.30;ReadPosRankSum=-0.014;TLOD=509.41;ANN=C|intron_variant|MODIFIER|CDC73|ENSG00000134371|transcript|ENST00000367435|protein_coding|12/16|c.1067-34_1067-32delATA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:229,194:0.468:423 0/0:156,0:0:156 | |
| chr1 195776651 . T A . PASS ClippingRankSum=0;DP=203;ECNT=1;FS=1.483;HCNT=34;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.54;ReadPosRankSum=-1.489;TLOD=10.16;ANN=A|intergenic_region|MODIFIER|AL357932.1-RP11-476B1.1|ENSG00000265108-ENSG00000227421|intergenic_region|ENSG00000265108-ENSG00000227421|||n.195776651T>A|||||| GT:AD:AF:DP 0/1:132,7:0.058:139 0/0:63,0:0:63 | |
| chr1 196712678 . G T . t_lod_fstar ClippingRankSum=0;DP=202;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=59.61;MQ0=0;MQRankSum=0.44;NLOD=15.04;ReadPosRankSum=-0.523;TLOD=4.71;ANN=T|missense_variant|MODERATE|CFH|ENSG00000000971|transcript|ENST00000367429|protein_coding|20/22|c.3230G>T|p.Cys1077Phe|3470/4127|3230/3696|1077/1231||,T|downstream_gene_variant|MODIFIER|CFH|ENSG00000000971|transcript|ENST00000470918|retained_intron||n.*2462G>T|||||2462|,T|non_coding_transcript_exon_variant|MODIFIER|CFH|ENSG00000000971|transcript|ENST00000466229|retained_intron|14/16|n.6328G>T|||||| GT:AD:AF:DP 0/1:129,5:0.033:134 0/0:68,0:0:68 | |
| chr1 197070491 . A G . t_lod_fstar ClippingRankSum=0;DP=122;ECNT=1;FS=2.085;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.83;ReadPosRankSum=1.67;TLOD=5.89;ANN=G|synonymous_variant|LOW|ASPM|ENSG00000066279|transcript|ENST00000367409|protein_coding|18/28|c.7890T>C|p.Ile2630Ile|8147/10887|7890/10434|2630/3477||,G|intron_variant|MODIFIER|ASPM|ENSG00000066279|transcript|ENST00000294732|protein_coding|17/26|c.4066-5197T>C||||||,G|intron_variant|MODIFIER|ASPM|ENSG00000066279|transcript|ENST00000367408|protein_coding|13/22|c.1816-5197T>C|||||| GT:AD:AF:DP 0/1:69,4:0.059:73 0/0:49,0:0:49 | |
| chr1 197141251 . C CTATA . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=493;ECNT=2;FS=0;HCNT=17;MAX_ED=2;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.54;ReadPosRankSum=1.771;TLOD=6.83;ANN=CTATA|intron_variant|MODIFIER|ZBTB41|ENSG00000177888|transcript|ENST00000367405|protein_coding|9/9|c.2074+35_2074+38dupTATA||||||,CTATA|intron_variant|MODIFIER|ZBTB41|ENSG00000177888|transcript|ENST00000467322|processed_transcript|10/10|n.2206+35_2206+38dupTATA|||||| GT:AD:AF:DP 0/1:260,7:0.016:267 0/0:81,5:0.018:86 | |
| chr1 197141253 . A C . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=492;ECNT=2;FS=0;HCNT=17;MAX_ED=2;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.75;ReadPosRankSum=0.558;TLOD=8.12;ANN=C|intron_variant|MODIFIER|ZBTB41|ENSG00000177888|transcript|ENST00000367405|protein_coding|9/9|c.2074+37T>G||||||,C|intron_variant|MODIFIER|ZBTB41|ENSG00000177888|transcript|ENST00000467322|processed_transcript|10/10|n.2206+37T>G|||||| GT:AD:AF:DP 0/1:324,8:0.026:332 0/0:136,4:0.031:140 | |
| chr1 200379078 . CCCG C . PASS ClippingRankSum=0;DP=609;ECNT=1;FS=0;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=32.21;ReadPosRankSum=-0.154;TLOD=6.35;ANN=C|5_prime_UTR_variant|MODIFIER|ZNF281|ENSG00000162702|transcript|ENST00000294740|protein_coding|1/2|c.-22_-20delCGG|||||246|,C|5_prime_UTR_variant|MODIFIER|ZNF281|ENSG00000162702|transcript|ENST00000367353|protein_coding|1/2|c.-26_-24delCGG|||||246|,C|5_prime_UTR_variant|MODIFIER|ZNF281|ENSG00000162702|transcript|ENST00000367352|protein_coding|1/3|c.-26_-24delCGG|||||246| GT:AD:AF:DP 0/1:390,4:0.011:394 0/0:195,2:0.015:197 | |
| chr1 200730181 . A ATTTTTTT . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=148;ECNT=5;FS=10.835;HCNT=8;MAX_ED=24;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.34;ReadPosRankSum=-0.245;TLOD=4.94;ANN=ATTTTTTT|frameshift_variant&stop_gained|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000236925|protein_coding|2/18|c.354_355insTTTTTTT|p.Lys119fs|404/7161|355/4470|119/1489||,ATTTTTTT|frameshift_variant&stop_gained|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000358823|protein_coding|2/17|c.354_355insTTTTTTT|p.Lys119fs|625/7352|355/4437|119/1478||,ATTTTTTT|frameshift_variant&stop_gained|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000413307|protein_coding|2/17|c.354_355insTTTTTTT|p.Lys119fs|404/4498|355/4389|119/1462||,ATTTTTTT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000236925|protein_coding|2/18|c.354_355insTTTTTTT||||||,ATTTTTTT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000358823|protein_coding|2/17|c.354_355insTTTTTTT||||||,ATTTTTTT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000413307|protein_coding|2/17|c.354_355insTTTTTTT||||||;LOF=(CAMSAP2|ENSG00000118200|6|0.50);NMD=(CAMSAP2|ENSG00000118200|6|0.50) GT:AD:AF:DP:PGT:PID 0/1:107,2:0.025:109:0|1:200730181_A_ATTTTTTT 0/0:38,1:0.028:39:0|1:200730181_A_ATTTTTTT | |
| chr1 200730183 . A ATT . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=147;ECNT=5;FS=10.746;HCNT=8;MAX_ED=24;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.43;TLOD=4.93;ANN=ATT|frameshift_variant|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000236925|protein_coding|2/18|c.356_357insTT|p.Lys119fs|406/7161|357/4470|119/1489||,ATT|frameshift_variant|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000358823|protein_coding|2/17|c.356_357insTT|p.Lys119fs|627/7352|357/4437|119/1478||,ATT|frameshift_variant|HIGH|CAMSAP2|ENSG00000118200|transcript|ENST00000413307|protein_coding|2/17|c.356_357insTT|p.Lys119fs|406/4498|357/4389|119/1462||,ATT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000236925|protein_coding|2/18|c.356_357insTT||||||,ATT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000358823|protein_coding|2/17|c.356_357insTT||||||,ATT|sequence_feature|LOW|CAMSAP2|ENSG00000118200|antibody-mapping:heterologous_protein_expression_evidence|ENST00000413307|protein_coding|2/17|c.356_357insTT||||||;LOF=(CAMSAP2|ENSG00000118200|6|0.50) GT:AD:AF:DP:PGT:PID 0/1:106,2:0.025:108:0|1:200730181_A_ATTTTTTT 0/0:38,1:0.03:39:0|1:200730181_A_ATTTTTTT | |
| chr1 200730191 . A T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=142;ECNT=5;FS=10.918;HCNT=8;MAX_ED=24;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.13;ReadPosRankSum=-1.086;TLOD=4.92;ANN=T|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000236925|protein_coding|2/18|c.364A>T|p.Thr122Ser|413/7161|364/4470|122/1489||,T|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000358823|protein_coding|2/17|c.364A>T|p.Thr122Ser|634/7352|364/4437|122/1478||,T|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000413307|protein_coding|2/17|c.364A>T|p.Thr122Ser|413/4498|364/4389|122/1462|| GT:AD:AF:DP:PGT:PID 0/1:103,2:0.024:105:0|1:200730181_A_ATTTTTTT 0/0:36,1:0.031:37:0|1:200730181_A_ATTTTTTT | |
| chr1 200730192 . C A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=142;ECNT=5;FS=11.133;HCNT=8;MAX_ED=24;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.13;ReadPosRankSum=-1.164;TLOD=4.97;ANN=A|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000236925|protein_coding|2/18|c.365C>A|p.Thr122Asn|414/7161|365/4470|122/1489||,A|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000358823|protein_coding|2/17|c.365C>A|p.Thr122Asn|635/7352|365/4437|122/1478||,A|missense_variant|MODERATE|CAMSAP2|ENSG00000118200|transcript|ENST00000413307|protein_coding|2/17|c.365C>A|p.Thr122Asn|414/4498|365/4389|122/1462|| GT:AD:AF:DP:PGT:PID 0/1:102,2:0.026:104:0|1:200730181_A_ATTTTTTT 0/0:37,1:0.031:38:0|1:200730181_A_ATTTTTTT | |
| chr1 200730205 . C A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=133;ECNT=5;FS=13.779;HCNT=8;MAX_ED=24;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.53;ReadPosRankSum=-2.556;TLOD=5.03;ANN=A|synonymous_variant|LOW|CAMSAP2|ENSG00000118200|transcript|ENST00000236925|protein_coding|2/18|c.378C>A|p.Leu126Leu|427/7161|378/4470|126/1489||,A|synonymous_variant|LOW|CAMSAP2|ENSG00000118200|transcript|ENST00000358823|protein_coding|2/17|c.378C>A|p.Leu126Leu|648/7352|378/4437|126/1478||,A|synonymous_variant|LOW|CAMSAP2|ENSG00000118200|transcript|ENST00000413307|protein_coding|2/17|c.378C>A|p.Leu126Leu|427/4498|378/4389|126/1462|| GT:AD:AF:DP:PGT:PID 0/1:96,2:0.028:98:0|1:200730181_A_ATTTTTTT 0/0:33,2:0.067:35:0|1:200730181_A_ATTTTTTT | |
| chr1 201180148 . A G . germline_risk ClippingRankSum=0;DP=20;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=38.69;MQ0=5;MQRankSum=-1.48;NLOD=0.602;ReadPosRankSum=2.2;TLOD=7.34;ANN=G|missense_variant|MODERATE|IGFN1|ENSG00000163395|transcript|ENST00000335211|protein_coding|12/24|c.6127A>G|p.Arg2043Gly|6257/11810|6127/11127|2043/3708||,G|5_prime_UTR_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000295591|protein_coding|12/23|c.-2394A>G|||||2394|,G|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000412892|protein_coding||c.-1623A>G|||||1622|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000473483|retained_intron||n.-2076A>G|||||2076|,G|downstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000444705|retained_intron||n.*4545A>G|||||4545|,G|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000451870|protein_coding|12/16|c.1242-2486A>G||||||,G|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000437879|nonsense_mediated_decay|12/25|c.1242-2486A>G|||||| GT:AD:AF:DP 0/1:4,2:0.333:6 0/0:3,0:0:3 | |
| chr1 201180269 . G A . germline_risk ClippingRankSum=0;DP=17;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=44.27;MQ0=3;MQRankSum=0.674;NLOD=0.903;ReadPosRankSum=-1.131;TLOD=9.88;ANN=A|missense_variant|MODERATE|IGFN1|ENSG00000163395|transcript|ENST00000335211|protein_coding|12/24|c.6248G>A|p.Gly2083Glu|6378/11810|6248/11127|2083/3708||,A|5_prime_UTR_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000295591|protein_coding|12/23|c.-2273G>A|||||2273|,A|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000412892|protein_coding||c.-1502G>A|||||1501|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000473483|retained_intron||n.-1955G>A|||||1955|,A|downstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000444705|retained_intron||n.*4666G>A|||||4666|,A|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000451870|protein_coding|12/16|c.1242-2365G>A||||||,A|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000437879|nonsense_mediated_decay|12/25|c.1242-2365G>A|||||| GT:AD:AF:DP 0/1:1,5:0.75:6 0/0:4,0:0:4 | |
| chr1 201180685 . A G . clustered_events ClippingRankSum=0;DP=32;ECNT=2;FS=0;HCNT=3;MAX_ED=8;MIN_ED=8;MQ=45.97;MQ0=7;MQRankSum=-3.362;NLOD=2.36;ReadPosRankSum=1.195;TLOD=8.05;ANN=G|missense_variant|MODERATE|IGFN1|ENSG00000163395|transcript|ENST00000335211|protein_coding|12/24|c.6664A>G|p.Lys2222Glu|6794/11810|6664/11127|2222/3708||,G|5_prime_UTR_premature_start_codon_gain_variant|LOW|IGFN1|ENSG00000163395|transcript|ENST00000295591|protein_coding|12/23|c.-1857A>G||||||,G|5_prime_UTR_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000295591|protein_coding|12/23|c.-1857A>G|||||1857|,G|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000412892|protein_coding||c.-1086A>G|||||1085|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000473483|retained_intron||n.-1539A>G|||||1539|,G|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000451870|protein_coding|12/16|c.1242-1949A>G||||||,G|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000437879|nonsense_mediated_decay|12/25|c.1242-1949A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:2,4:0.667:6:0|1:201180685_A_G 0/0:12,0:0:12:0|1:201180685_A_G | |
| chr1 201180693 . G A . clustered_events ClippingRankSum=0;DP=32;ECNT=2;FS=0;HCNT=3;MAX_ED=8;MIN_ED=8;MQ=47.79;MQ0=6;MQRankSum=-3.399;NLOD=3.11;ReadPosRankSum=0.29;TLOD=7.71;ANN=A|missense_variant|MODERATE|IGFN1|ENSG00000163395|transcript|ENST00000335211|protein_coding|12/24|c.6672G>A|p.Met2224Ile|6802/11810|6672/11127|2224/3708||,A|5_prime_UTR_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000295591|protein_coding|12/23|c.-1849G>A|||||1849|,A|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000412892|protein_coding||c.-1078G>A|||||1077|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000473483|retained_intron||n.-1531G>A|||||1531|,A|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000451870|protein_coding|12/16|c.1242-1941G>A||||||,A|intron_variant|MODIFIER|IGFN1|ENSG00000163395|transcript|ENST00000437879|nonsense_mediated_decay|12/25|c.1242-1941G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:2,3:0.5:5:0|1:201180685_A_G 0/0:14,0:0:14:0|1:201180685_A_G | |
| chr1 201778653 . C T . germline_risk ClippingRankSum=0;DP=24;ECNT=1;FS=1.893;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.11;ReadPosRankSum=-1.258;TLOD=14.39;ANN=T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000367296|protein_coding|22/30|c.4389C>T|p.Phe1463Phe|4809/13091|4389/5634|1463/1877||,T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000367302|protein_coding|22/30|c.4248C>T|p.Phe1416Phe|4482/9139|4248/5493|1416/1830||,T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000295624|protein_coding|21/29|c.4380C>T|p.Phe1460Phe|4727/13014|4380/5625|1460/1874||,T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000367297|protein_coding|21/29|c.4365C>T|p.Phe1455Phe|4712/12999|4365/5610|1455/1869||,T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000367300|protein_coding|20/28|c.4209C>T|p.Phe1403Phe|4556/12843|4209/5454|1403/1817||,T|synonymous_variant|LOW|NAV1|ENSG00000134369|transcript|ENST00000367295|protein_coding|19/27|c.3207C>T|p.Phe1069Phe|3363/11645|3207/4452|1069/1483||,T|downstream_gene_variant|MODIFIER|MIR1231|ENSG00000221028|transcript|ENST00000408101|miRNA||n.*823C>T|||||823|,T|downstream_gene_variant|MODIFIER|NAV1|ENSG00000134369|transcript|ENST00000438083|protein_coding||c.*1480C>T|||||1480|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|IPO9-AS1|ENSG00000231871|transcript|ENST00000413035|antisense|2/2|n.684+7702G>A|||||| GT:AD:AF:DP 0/1:7,8:0.455:15 0/0:9,0:0:9 | |
| chr1 202097524 . ACTG A . PASS ClippingRankSum=0;DP=181;ECNT=1;FS=1.31;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60.06;MQ0=0;MQRankSum=-0.217;NLOD=13.77;ReadPosRankSum=0.152;TLOD=11.64;ANN=A|disruptive_inframe_deletion|MODERATE|GPR37L1|ENSG00000170075|transcript|ENST00000367282|protein_coding|2/2|c.1305_1307delCTG|p.Cys436del|1411/6588|1305/1446|435/481||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:96,9:0.087:105 0/0:60,0:0:60 | |
| chr1 203821496 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=835;ECNT=2;FS=0;HCNT=3;MAX_ED=12;MIN_ED=12;MQ=59.22;MQ0=1;MQRankSum=-6.478;NLOD=55.13;ReadPosRankSum=-1.362;TLOD=5.83;ANN=C|missense_variant|MODERATE|ZC3H11A|ENSG00000058673|transcript|ENST00000332127|protein_coding|20/20|c.2402T>C|p.Leu801Pro|3259/5015|2402/2433|801/810||,C|missense_variant|MODERATE|ZC3H11A|ENSG00000058673|transcript|ENST00000367214|protein_coding|20/20|c.2402T>C|p.Leu801Pro|3399/3451|2402/2433|801/810||,C|missense_variant|MODERATE|ZC3H11A|ENSG00000058673|transcript|ENST00000367212|protein_coding|20/20|c.2402T>C|p.Leu801Pro|2942/3004|2402/2433|801/810||,C|missense_variant|MODERATE|ZC3H11A|ENSG00000058673|transcript|ENST00000545588|protein_coding|17/17|c.2402T>C|p.Leu801Pro|6229/7979|2402/2433|801/810||,C|missense_variant|MODERATE|ZC3H11A|ENSG00000058673|transcript|ENST00000367210|protein_coding|17/17|c.2402T>C|p.Leu801Pro|2615/4365|2402/2433|801/810||,C|3_prime_UTR_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000495527|nonsense_mediated_decay|17/17|c.*463T>C|||||1854|,C|downstream_gene_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000453771|protein_coding||c.*4681T>C|||||4681|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000488411|processed_transcript||n.*1246T>C|||||1246| GT:AD:AF:DP:PGT:PID 0/1:558,3:0.007481:561:0|1:203821496_T_C 0/0:263,2:0.005128:265:0|1:203821496_T_C | |
| chr1 203821508 . C G . clustered_events;t_lod_fstar ClippingRankSum=0;DP=831;ECNT=2;FS=0;HCNT=3;MAX_ED=12;MIN_ED=12;MQ=59.15;MQ0=1;MQRankSum=-9.055;NLOD=58.35;ReadPosRankSum=0.814;TLOD=5.82;ANN=G|stop_gained|HIGH|ZC3H11A|ENSG00000058673|transcript|ENST00000332127|protein_coding|20/20|c.2414C>G|p.Ser805*|3271/5015|2414/2433|805/810||,G|stop_gained|HIGH|ZC3H11A|ENSG00000058673|transcript|ENST00000367214|protein_coding|20/20|c.2414C>G|p.Ser805*|3411/3451|2414/2433|805/810||,G|stop_gained|HIGH|ZC3H11A|ENSG00000058673|transcript|ENST00000367212|protein_coding|20/20|c.2414C>G|p.Ser805*|2954/3004|2414/2433|805/810||,G|stop_gained|HIGH|ZC3H11A|ENSG00000058673|transcript|ENST00000545588|protein_coding|17/17|c.2414C>G|p.Ser805*|6241/7979|2414/2433|805/810||,G|stop_gained|HIGH|ZC3H11A|ENSG00000058673|transcript|ENST00000367210|protein_coding|17/17|c.2414C>G|p.Ser805*|2627/4365|2414/2433|805/810||,G|3_prime_UTR_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000495527|nonsense_mediated_decay|17/17|c.*475C>G|||||1866|,G|downstream_gene_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000453771|protein_coding||c.*4693C>G|||||4693|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|ZC3H11A|ENSG00000058673|transcript|ENST00000488411|processed_transcript||n.*1258C>G|||||1258| GT:AD:AF:DP:PGT:PID 0/1:553,3:0.007426:556:0|1:203821496_T_C 0/0:264,0:0:264:0|1:203821496_T_C | |
| chr1 204379059 . G T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=88;ECNT=7;FS=14.776;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=1.276;TLOD=5.30;ANN=T|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1481C>A|p.Ala494Glu|1861/5227|1481/2142|494/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25406G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:62,3:0.038:65:0|1:204379059_G_T 0/0:23,0:0:23:0|1:204379059_G_T | |
| chr1 204379060 . C T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=88;ECNT=7;FS=14.776;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=1.206;TLOD=5.30;ANN=T|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1480G>A|p.Ala494Thr|1860/5227|1480/2142|494/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25405C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:62,3:0.038:65:0|1:204379059_G_T 0/0:23,0:0:23:0|1:204379059_G_T | |
| chr1 204379062 . G T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=88;ECNT=7;FS=14.776;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=1.076;TLOD=5.27;ANN=T|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1478C>A|p.Thr493Lys|1858/5227|1478/2142|493/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25403G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:63,3:0.036:66:0|1:204379059_G_T 0/0:22,0:0:22:0|1:204379059_G_T | |
| chr1 204379066 . A T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=89;ECNT=7;FS=14.925;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.62;ReadPosRankSum=0.981;TLOD=5.29;ANN=T|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1474T>A|p.Phe492Ile|1854/5227|1474/2142|492/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25399A>T|||||| GT:AD:AF:DP:PGT:PID 0/1:64,3:0.037:67:0|1:204379059_G_T 0/0:22,0:0.045:22:0|1:204379059_G_T | |
| chr1 204379070 . C A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=87;ECNT=7;FS=21.032;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.32;ReadPosRankSum=-0.376;TLOD=5.25;ANN=A|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1470G>T|p.Gln490His|1850/5227|1470/2142|490/713||,A|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25395C>A|||||| GT:AD:AF:DP:PGT:PID 0/1:63,3:0.036:66:0|1:204379059_G_T 0/0:20,1:0.048:21:0|1:204379059_G_T | |
| chr1 204379082 . A T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=98;ECNT=7;FS=17.4;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.80;ReadPosRankSum=-0.558;TLOD=5.19;ANN=T|synonymous_variant|LOW|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1458T>A|p.Pro486Pro|1838/5227|1458/2142|486/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25383A>T|||||| GT:AD:AF:DP:PGT:PID 0/1:74,3:0.033:77:0|1:204379082_A_T 0/0:19,0:0.053:19:0|1:204379082_A_T | |
| chr1 204379083 . G T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=100;ECNT=7;FS=23.135;HCNT=41;MAX_ED=24;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.80;ReadPosRankSum=-1.383;TLOD=5.19;ANN=T|missense_variant|MODERATE|PPP1R15B|ENSG00000158615|transcript|ENST00000367188|protein_coding|1/2|c.1457C>A|p.Pro486His|1837/5227|1457/2142|486/713||,T|intron_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense|1/2|n.147-25382G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:74,3:0.033:77:0|1:204379082_A_T 0/0:20,1:0.053:21:0|1:204379082_A_T | |
| chr1 204408021 . G A . t_lod_fstar ClippingRankSum=0;DP=63;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.51;ReadPosRankSum=-0.658;TLOD=4.63;ANN=A|downstream_gene_variant|MODIFIER|RP11-739N20.2|ENSG00000226330|transcript|ENST00000443515|antisense||n.*3047G>A|||||3047|,A|intron_variant|MODIFIER|PIK3C2B|ENSG00000133056|transcript|ENST00000367187|protein_coding|24/33|c.3516+42C>T||||||,A|intron_variant|MODIFIER|PIK3C2B|ENSG00000133056|transcript|ENST00000424712|protein_coding|25/34|c.3432+42C>T|||||| GT:AD:AF:DP 0/1:40,3:0.063:43 0/0:20,0:0:20 | |
| chr1 204507128 . T C . PASS ClippingRankSum=0;DP=117;ECNT=1;FS=0.773;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.81;ReadPosRankSum=1.692;TLOD=41.43;ANN=C|upstream_gene_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000444261|protein_coding||c.-4789T>C|||||4789|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000367180|protein_coding||c.*1081T>C|||||959|,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000367182|protein_coding|6/10|c.412-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000463049|processed_transcript|6/10|n.522-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000507825|protein_coding|5/8|c.343+5754T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000470908|processed_transcript|5/8|n.438-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000471783|processed_transcript|3/5|n.227-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000454264|protein_coding|6/9|c.412-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000367183|protein_coding|2/2|c.79-11266T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000391947|protein_coding|4/8|c.344-209T>C||||||,C|intron_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000367179|protein_coding|1/5|c.78+9T>C||||||WARNING_TRANSCRIPT_INCOMPLETE,C|non_coding_transcript_exon_variant|MODIFIER|MDM4|ENSG00000198625|transcript|ENST00000462012|processed_transcript|1/2|n.126T>C|||||| GT:AD:AF:DP 0/1:38,36:0.48:74 0/0:39,0:0:39 | |
| chr1 206858909 . A C . t_lod_fstar ClippingRankSum=0;DP=74;ECNT=1;FS=11.068;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.75;ReadPosRankSum=-0.757;TLOD=4.98;ANN=C|downstream_gene_variant|MODIFIER|SNORD112|ENSG00000252853|transcript|ENST00000517044|snoRNA||n.*3529A>C|||||3529|,C|downstream_gene_variant|MODIFIER|DYRK3|ENSG00000143479|transcript|ENST00000489878|processed_transcript||n.*1145A>C|||||1145|,C|intron_variant|MODIFIER|MAPKAPK2|ENSG00000162889|transcript|ENST00000367103|protein_coding|1/9|c.279+56A>C||||||,C|intron_variant|MODIFIER|MAPKAPK2|ENSG00000162889|transcript|ENST00000294981|protein_coding|1/9|c.279+56A>C|||||| GT:AD:AF:DP 0/1:25,6:0.2:31 0/0:37,0:0:37 | |
| chr1 207809473 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=119;ECNT=2;FS=4.925;HCNT=29;MAX_ED=11;MIN_ED=11;MQ=58.94;MQ0=0;MQRankSum=-9.569;NLOD=4.25;ReadPosRankSum=-2.9;TLOD=7.81;ANN=C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367049|protein_coding|46/46|c.7458-3269T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367051|protein_coding|38/38|c.6108-3269T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367052|protein_coding|38/38|c.6108-3269T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367053|protein_coding|38/38|c.6108-3269T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000400960|protein_coding|38/38|c.6108-3269T>C|||||| GT:AD:AF:DP 0/1:81,4:0.066:85 0/0:31,1:0.038:32 | |
| chr1 207809484 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=143;ECNT=2;FS=1.13;HCNT=25;MAX_ED=11;MIN_ED=11;MQ=58.24;MQ0=0;MQRankSum=-7.712;NLOD=0.602;ReadPosRankSum=-4.313;TLOD=8.72;ANN=C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367049|protein_coding|46/46|c.7458-3258T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367051|protein_coding|38/38|c.6108-3258T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367052|protein_coding|38/38|c.6108-3258T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000367053|protein_coding|38/38|c.6108-3258T>C||||||,C|intron_variant|MODIFIER|CR1|ENSG00000203710|transcript|ENST00000400960|protein_coding|38/38|c.6108-3258T>C|||||| GT:AD:AF:DP 0/1:83,8:0.094:91 0/0:42,6:0.111:48 | |
| chr1 208218503 . A G . t_lod_fstar ClippingRankSum=0;DP=136;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.23;ReadPosRankSum=-1.172;TLOD=4.13;ANN=G|missense_variant|MODERATE|PLXNA2|ENSG00000076356|transcript|ENST00000367033|protein_coding|19/32|c.3548T>C|p.Val1183Ala|4306/11444|3548/5685|1183/1894||,G|upstream_gene_variant|MODIFIER|PLXNA2|ENSG00000076356|transcript|ENST00000463510|processed_transcript||n.-4894T>C|||||4894| GT:AD:AF:DP 0/1:93,1:0.032:94 0/0:42,0:0:42 | |
| chr1 209628838 . G T . t_lod_fstar ClippingRankSum=0;DP=263;ECNT=1;FS=0;HCNT=45;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.37;ReadPosRankSum=-0.095;TLOD=4.58;ANN=T|intergenic_region|MODIFIER|MIR205HG-RP1-272L16.1|ENSG00000230937-ENSG00000224260|intergenic_region|ENSG00000230937-ENSG00000224260|||n.209628838G>T|||||| GT:AD:AF:DP 0/1:185,4:0.024:189 0/0:72,2:0.019:74 | |
| chr1 211590237 . G T . t_lod_fstar ClippingRankSum=0;DP=48;ECNT=1;FS=0;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.91;ReadPosRankSum=0.542;TLOD=4.11;ANN=T|upstream_gene_variant|MODIFIER|SNX25P1|ENSG00000236809|transcript|ENST00000441817|unprocessed_pseudogene||n.-130G>T|||||130|,T|intron_variant|MODIFIER|LINC00467|ENSG00000153363|transcript|ENST00000423222|processed_transcript|4/5|n.421-9316G>T|||||| GT:AD:AF:DP 0/1:30,2:0.087:32 0/0:16,0:0:16 | |
| chr1 212482476 . G T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=45;ECNT=10;FS=0;HCNT=26;MAX_ED=103;MIN_ED=13;MQ=56.29;MQ0=2;MQRankSum=-6.264;NLOD=2.41;ReadPosRankSum=0.441;TLOD=6.14;ANN=T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-20001G>T||||||,T|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9509C>A||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7042G>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7042G>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2234G>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4633G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.385C>A|||||| GT:AD:AF:DP 0/1:28,3:0.095:31 0/0:10,0:0:10 | |
| chr1 212482489 . G C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=47;ECNT=10;FS=0;HCNT=25;MAX_ED=103;MIN_ED=13;MQ=56.11;MQ0=2;MQRankSum=-5.487;NLOD=2.41;ReadPosRankSum=0.545;TLOD=6.09;ANN=C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19988G>C||||||,C|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9522C>G||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7055G>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7055G>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2247G>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4620G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.372C>G|||||| GT:AD:AF:DP:PGT:PID 0/1:30,3:0.091:33:0|1:212482489_G_C 0/0:10,0:0:10:0|1:212482489_G_C | |
| chr1 212482496 . G A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=49;ECNT=10;FS=0;HCNT=25;MAX_ED=103;MIN_ED=13;MQ=55.61;MQ0=3;MQRankSum=-5.555;NLOD=2.71;ReadPosRankSum=0.497;TLOD=6.05;ANN=A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19981G>A||||||,A|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9529C>T||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7062G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7062G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2254G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4613G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.365C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:31,3:0.087:34:0|1:212482489_G_C 0/0:10,0:0:10:0|1:212482489_G_C | |
| chr1 212482503 . T C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=50;ECNT=10;FS=3.029;HCNT=25;MAX_ED=103;MIN_ED=13;MQ=55.39;MQ0=4;MQRankSum=-5.222;NLOD=3.01;ReadPosRankSum=1.905;TLOD=6.01;ANN=C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19974T>C||||||,C|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9536A>G||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7069T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7069T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2261T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4606T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.358A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:29,2:0.083:31:0|1:212482489_G_C 0/0:13,0:0:13:0|1:212482489_G_C | |
| chr1 212482504 . G A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=52;ECNT=10;FS=3.031;HCNT=25;MAX_ED=103;MIN_ED=13;MQ=55.55;MQ0=4;MQRankSum=-4.683;NLOD=3.01;ReadPosRankSum=1.978;TLOD=6.05;ANN=A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19973G>A||||||,A|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9537C>T||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7070G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7070G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2262G>A||||||,A|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4605G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.357C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:31,2:0.087:33:0|1:212482489_G_C 0/0:13,0:0:13:0|1:212482489_G_C | |
| chr1 212482534 . A G . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=63;ECNT=10;FS=6.247;HCNT=20;MAX_ED=103;MIN_ED=13;MQ=57.22;MQ0=4;MQRankSum=-4.812;NLOD=3.61;ReadPosRankSum=1.509;TLOD=5.70;ANN=G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19943A>G||||||,G|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9567T>C||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7100A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7100A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2292A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4575A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.327T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:41,2:0.059:43:0|1:212482534_A_G 0/0:16,0:0:16:0|1:212482534_A_G | |
| chr1 212482536 . T C . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=63;ECNT=10;FS=6.394;HCNT=20;MAX_ED=103;MIN_ED=13;MQ=57.72;MQ0=3;MQRankSum=-4.854;NLOD=3.61;ReadPosRankSum=1.401;TLOD=5.70;ANN=C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19941T>C||||||,C|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9569A>G||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7102T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7102T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2294T>C||||||,C|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4573T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.325A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:42,2:0.059:44:0|1:212482534_A_G 0/0:16,0:0:16:0|1:212482534_A_G | |
| chr1 212482561 . C T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=68;ECNT=10;FS=6.66;HCNT=21;MAX_ED=103;MIN_ED=13;MQ=57.43;MQ0=4;MQRankSum=-5.016;NLOD=3.31;ReadPosRankSum=-0.927;TLOD=5.65;ANN=T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19916C>T||||||,T|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9594G>A||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7127C>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7127C>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2319C>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4548C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.300G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:46,2:0.056:48:0|1:212482561_C_T 0/0:16,0:0:16:0|1:212482561_C_T | |
| chr1 212482562 . A T . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=67;ECNT=10;FS=6.522;HCNT=21;MAX_ED=103;MIN_ED=13;MQ=57.39;MQ0=4;MQRankSum=-4.976;NLOD=3.61;ReadPosRankSum=-1;TLOD=5.65;ANN=T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19915A>T||||||,T|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9595T>A||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7128A>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7128A>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2320A>T||||||,T|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4547A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.299T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:46,2:0.056:48:0|1:212482561_C_T 0/0:15,0:0:15:0|1:212482561_C_T | |
| chr1 212482579 . A G . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=79;ECNT=10;FS=6.998;HCNT=19;MAX_ED=103;MIN_ED=13;MQ=56.2;MQ0=8;MQRankSum=-5.288;NLOD=4.51;ReadPosRankSum=-1.999;TLOD=5.65;ANN=G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000261461|protein_coding|1/12|c.182-19898A>G||||||,G|intron_variant|MODIFIER|RP11-384C4.7|ENSG00000234915|transcript|ENST00000442146|antisense|1/1|n.257-9612T>C||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000537030|protein_coding|1/12|c.10+7145A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498123|processed_transcript|1/1|n.230+7145A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000479259|processed_transcript|2/4|n.348+2337A>G||||||,G|intron_variant|MODIFIER|PPP2R5A|ENSG00000066027|transcript|ENST00000498129|processed_transcript|1/6|n.231-4530A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|RP11-384C4.3|ENSG00000225338|transcript|ENST00000416139|processed_pseudogene|1/1|n.282T>C|||||| GT:AD:AF:DP 0/1:49,2:0.056:51 0/0:20,0:0:20 | |
| chr1 212798405 . G T . t_lod_fstar ClippingRankSum=0;DP=100;ECNT=1;FS=0;HCNT=60;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=-1.349;TLOD=5.24;ANN=T|synonymous_variant|LOW|FAM71A|ENSG00000162771|transcript|ENST00000294829|protein_coding|1/1|c.186G>T|p.Val62Val|617/2332|186/1785|62/594||,T|downstream_gene_variant|MODIFIER|ATF3|ENSG00000162772|transcript|ENST00000341491|protein_coding||c.*5508G>T|||||4286|,T|downstream_gene_variant|MODIFIER|ATF3|ENSG00000162772|transcript|ENST00000366987|protein_coding||c.*5508G>T|||||4291|,T|downstream_gene_variant|MODIFIER|ATF3|ENSG00000162772|transcript|ENST00000492118|processed_transcript||n.*4286G>T|||||4286|,T|intron_variant|MODIFIER|RP11-338C15.5|ENSG00000235862|transcript|ENST00000427949|antisense|1/1|n.1539-93C>A|||||| GT:AD:AF:DP 0/1:65,4:0.061:69 0/0:31,0:0:31 | |
| chr1 216371934 . A C . germline_risk ClippingRankSum=0;DP=60;ECNT=1;FS=1.516;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.11;ReadPosRankSum=0.115;TLOD=12.77;ANN=C|splice_region_variant&intron_variant|LOW|USH2A|ENSG00000042781|transcript|ENST00000366943|protein_coding|17/72|c.3812-8T>G||||||,C|splice_region_variant&intron_variant|LOW|USH2A|ENSG00000042781|transcript|ENST00000307340|protein_coding|17/71|c.3812-8T>G||||||,C|splice_region_variant&intron_variant|LOW|USH2A|ENSG00000042781|transcript|ENST00000366942|protein_coding|17/20|c.3812-8T>G||||||,C|downstream_gene_variant|MODIFIER|MRPS18BP1|ENSG00000226013|transcript|ENST00000414228|processed_pseudogene||n.*3043T>G|||||3043|,C|intron_variant|MODIFIER|RP5-1099E6.3|ENSG00000236292|transcript|ENST00000420867|antisense|2/2|n.362+2667A>C|||||| GT:AD:AF:DP 0/1:39,9:0.2:48 0/0:12,0:0:12 | |
| chr1 216676843 . TTTA T . PASS ClippingRankSum=0;DP=466;ECNT=1;FS=2.518;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.18;ReadPosRankSum=-2.24;TLOD=17.88;ANN=T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366937|protein_coding|8/8|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000361525|protein_coding|9/9|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366940|protein_coding|9/9|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000391890|protein_coding|9/9|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000408911|protein_coding|7/7|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000360012|protein_coding|7/7|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000361395|protein_coding|8/8|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366938|protein_coding|8/8|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000359162|protein_coding|8/8|c.*3435_*3437delTAA|||||3435|,T|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000493603|protein_coding|9/9|c.*3435_*3437delTAA|||||3435|,T|downstream_gene_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000463665|protein_coding||c.*3435_*3437delTAA|||||1952|,T|downstream_gene_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000487276|protein_coding||c.*3435_*3437delTAA|||||1988|,T|downstream_gene_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000493748|protein_coding||c.*3435_*3437delTAA|||||3286| GT:AD:AF:DP 0/1:288,10:0.037:298 0/0:97,2:0.014:99 | |
| chr1 216680240 . T C . t_lod_fstar ClippingRankSum=0;DP=144;ECNT=1;FS=1.78;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.03;ReadPosRankSum=1.383;TLOD=4.32;ANN=C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366937|protein_coding|8/8|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000361525|protein_coding|9/9|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366940|protein_coding|9/9|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000391890|protein_coding|9/9|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000408911|protein_coding|7/7|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000360012|protein_coding|7/7|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000361395|protein_coding|8/8|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000366938|protein_coding|8/8|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000359162|protein_coding|8/8|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000493603|protein_coding|9/9|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000463665|protein_coding|8/8|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000487276|protein_coding|9/9|c.*41A>G|||||41|,C|3_prime_UTR_variant|MODIFIER|ESRRG|ENSG00000196482|transcript|ENST00000493748|protein_coding|9/9|c.*41A>G|||||41| GT:AD:AF:DP 0/1:98,5:0.045:103 0/0:41,0:0:41 | |
| chr1 222923187 . G A . t_lod_fstar ClippingRankSum=0;DP=91;ECNT=1;FS=1.812;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=-0.028;TLOD=5.42;ANN=A|downstream_gene_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000434700|protein_coding||c.*321G>A|||||321|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000460763|retained_intron||n.*2398G>A|||||2398|,A|downstream_gene_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000456298|protein_coding||c.*324G>A|||||324|WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000360827|protein_coding|5/5|c.340-76G>A||||||,A|intron_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000445590|protein_coding|5/5|c.340-76G>A||||||,A|intron_variant|MODIFIER|FAM177B|ENSG00000197520|transcript|ENST00000391880|nonsense_mediated_decay|5/5|c.*481-76G>A|||||| GT:AD:AF:DP 0/1:61,5:0.065:66 0/0:25,0:0:25 | |
| chr1 223152946 . GT G . t_lod_fstar ClippingRankSum=0;DP=99;ECNT=1;FS=6.24;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60.11;MQ0=0;MQRankSum=3.937;NLOD=7.51;ReadPosRankSum=-0.816;TLOD=5.61;ANN=G|intron_variant|MODIFIER|DISP1|ENSG00000154309|transcript|ENST00000284476|protein_coding|2/7|c.510-3471delT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DISP1|ENSG00000154309|transcript|ENST00000495684|processed_transcript|3/7|n.163-3471delT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DISP1|ENSG00000154309|transcript|ENST00000360254|protein_coding|3/3|c.510-13delT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:54,6:0.091:60 0/0:37,0:0:37 | |
| chr1 223536702 . TTGC T . PASS ClippingRankSum=0;DP=108;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.90;ReadPosRankSum=0.641;TLOD=8.55;ANN=T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000343846|protein_coding|1/8|c.63_65delGCA|p.Gln22del|699/3480|63/1473|21/490||,T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000366878|protein_coding|2/9|c.63_65delGCA|p.Gln22del|246/3025|63/1473|21/490||,T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000484758|protein_coding|2/8|c.63_65delGCA|p.Gln22del|174/2736|63/1266|21/421||,T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000494793|protein_coding|2/9|c.63_65delGCA|p.Gln22del|222/1833|63/1467|21/488||,T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000344029|protein_coding|2/6|c.63_65delGCA|p.Gln22del|211/1056|63/873|21/290||,T|disruptive_inframe_deletion|MODERATE|SUSD4|ENSG00000143502|transcript|ENST00000366877|protein_coding|2/4|c.63_65delGCA|p.Gln22del|246/502|63/321|21/106||,T|5_prime_UTR_variant|MODIFIER|SUSD4|ENSG00000143502|transcript|ENST00000454695|protein_coding|2/10|c.-573_-571delGCA|||||94805|,T|upstream_gene_variant|MODIFIER|SUSD4|ENSG00000143502|transcript|ENST00000608996|protein_coding||c.-28_-26delGCA|||||24|WARNING_TRANSCRIPT_NO_START_CODON,T|non_coding_transcript_exon_variant|MODIFIER|SUSD4|ENSG00000143502|transcript|ENST00000478605|processed_transcript|2/7|n.125_127delGCA||||||,T|non_coding_transcript_exon_variant|MODIFIER|SUSD4|ENSG00000143502|transcript|ENST00000483818|processed_transcript|2/6|n.125_127delGCA||||||,T|non_coding_transcript_exon_variant|MODIFIER|SUSD4|ENSG00000143502|transcript|ENST00000342943|processed_transcript|2/4|n.236_238delGCA|||||| GT:AD:AF:DP 0/1:58,3:0.079:61 0/0:30,0:0:30 | |
| chr1 224194194 . AATAC A . PASS ClippingRankSum=0;DP=183;ECNT=1;FS=0;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.72;ReadPosRankSum=-0.72;TLOD=6.62;ANN=A|upstream_gene_variant|MODIFIER|RP11-504P24.4|ENSG00000185495|transcript|ENST00000540997|lincRNA||n.-2234_-2231delATAC|||||2234|,A|upstream_gene_variant|MODIFIER|RP11-504P24.6|ENSG00000263182|transcript|ENST00000572124|lincRNA||n.-2234_-2231delATAC|||||2234|,A|downstream_gene_variant|MODIFIER|RP11-504P24.3|ENSG00000243000|transcript|ENST00000327086|unprocessed_pseudogene||n.*2839_*2842delATAC|||||2839|,A|intron_variant|MODIFIER|RP11-504P24.4|ENSG00000185495|transcript|ENST00000449219|lincRNA|3/3|n.375-2810_375-2807delTACA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:117,4:0.038:121 0/0:47,3:0.051:50 | |
| chr1 225600164 . G A . t_lod_fstar ClippingRankSum=0;DP=139;ECNT=1;FS=1.911;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.67;ReadPosRankSum=-1.305;TLOD=4.09;ANN=A|missense_variant|MODERATE|LBR|ENSG00000143815|transcript|ENST00000272163|protein_coding|8/14|c.1076C>T|p.Ala359Val|1172/3745|1076/1848|359/615||,A|missense_variant|MODERATE|LBR|ENSG00000143815|transcript|ENST00000338179|protein_coding|8/14|c.1076C>T|p.Ala359Val|1202/3774|1076/1848|359/615||,A|upstream_gene_variant|MODIFIER|AC092811.1|ENSG00000203691|transcript|ENST00000366845|protein_coding||c.-1412G>A|||||240|,A|upstream_gene_variant|MODIFIER|LBR|ENSG00000143815|transcript|ENST00000424022|protein_coding||c.-1045C>T|||||1045|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:108,4:0.041:112 0/0:27,0:0:27 | |
| chr1 225683824 . T A . PASS ClippingRankSum=0;DP=352;ECNT=1;FS=1.017;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=23.77;ReadPosRankSum=-0.116;TLOD=131.27;ANN=A|3_prime_UTR_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000366844|protein_coding|15/15|c.*1653A>T|||||1653|,A|downstream_gene_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000284563|protein_coding||c.*1653A>T|||||1277|,A|downstream_gene_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000366843|protein_coding||c.*1653A>T|||||963|,A|downstream_gene_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000498108|retained_intron||n.*1301A>T|||||1301|,A|downstream_gene_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000483952|retained_intron||n.*1512A>T|||||1512|,A|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000488523|processed_transcript|4/4|n.214+2225A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000358675|retained_intron|9/9|n.3013A>T|||||| GT:AD:AF:DP 0/1:168,71:0.311:239 0/0:111,0:0:111 | |
| chr1 225718776 . GGA G . t_lod_fstar ClippingRankSum=0;DP=212;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.65;ReadPosRankSum=-0.343;TLOD=5.32;ANN=G|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000284563|protein_coding|4/14|c.407-438_407-437delTC||||||,G|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000366844|protein_coding|3/14|c.350-438_350-437delTC||||||,G|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000366843|protein_coding|3/13|c.350-438_350-437delTC||||||,G|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000497899|retained_intron|1/2|n.179-438_179-437delTC||||||,G|intron_variant|MODIFIER|ENAH|ENSG00000154380|transcript|ENST00000391874|processed_transcript|3/4|n.436-438_436-437delTC|||||| GT:AD:AF:DP 0/1:138,3:0.034:141 0/0:56,1:0.024:57 | |
| chr1 226259111 . T C . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=352;ECNT=2;FS=27.601;HCNT=4;MAX_ED=2;MIN_ED=2;MQ=51.66;MQ0=24;MQRankSum=-3.848;NLOD=8.75;ReadPosRankSum=-3.21;TLOD=22.74;ANN=C|synonymous_variant|LOW|H3F3A|ENSG00000163041|transcript|ENST00000366813|protein_coding|3/3|c.342T>C|p.His114His|717/1308|342/411|114/136||,C|synonymous_variant|LOW|H3F3A|ENSG00000163041|transcript|ENST00000366816|protein_coding|5/5|c.342T>C|p.His114His|686/799|342/411|114/136||,C|synonymous_variant|LOW|H3F3A|ENSG00000163041|transcript|ENST00000366815|protein_coding|4/4|c.342T>C|p.His114His|499/1088|342/411|114/136||,C|downstream_gene_variant|MODIFIER|H3F3A|ENSG00000163041|transcript|ENST00000366814|protein_coding||c.*5511T>C|||||4141| GT:AD:AF:DP:PGT:PID 0/1:191,9:0.058:200:0|1:226259111_T_C 0/0:97,3:0.044:100:0|1:226259111_T_C | |
| chr1 226259113 . C G . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=347;ECNT=2;FS=27.868;HCNT=4;MAX_ED=2;MIN_ED=2;MQ=51.53;MQ0=24;MQRankSum=-3.791;NLOD=8.75;ReadPosRankSum=-2.958;TLOD=22.69;ANN=G|missense_variant|MODERATE|H3F3A|ENSG00000163041|transcript|ENST00000366813|protein_coding|3/3|c.344C>G|p.Ala115Gly|719/1308|344/411|115/136||,G|missense_variant|MODERATE|H3F3A|ENSG00000163041|transcript|ENST00000366816|protein_coding|5/5|c.344C>G|p.Ala115Gly|688/799|344/411|115/136||,G|missense_variant|MODERATE|H3F3A|ENSG00000163041|transcript|ENST00000366815|protein_coding|4/4|c.344C>G|p.Ala115Gly|501/1088|344/411|115/136||,G|downstream_gene_variant|MODIFIER|H3F3A|ENSG00000163041|transcript|ENST00000366814|protein_coding||c.*5513C>G|||||4143| GT:AD:AF:DP:PGT:PID 0/1:187,9:0.057:196:0|1:226259111_T_C 0/0:96,3:0.044:99:0|1:226259111_T_C | |
| chr1 228431131 . G T . t_lod_fstar ClippingRankSum=0;DP=72;ECNT=1;FS=3.388;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=-0.241;TLOD=4.19;ANN=T|missense_variant|MODERATE|OBSCN|ENSG00000154358|transcript|ENST00000570156|protein_coding|11/116|c.3453G>T|p.Gln1151His|3527/26927|3453/26772|1151/8923||,T|missense_variant|MODERATE|OBSCN|ENSG00000154358|transcript|ENST00000284548|protein_coding|10/81|c.3177G>T|p.Gln1059His|3251/20432|3177/19863|1059/6620||,T|missense_variant|MODERATE|OBSCN|ENSG00000154358|transcript|ENST00000422127|protein_coding|10/105|c.3177G>T|p.Gln1059His|3221/24030|3177/23907|1059/7968||,T|5_prime_UTR_variant|MODIFIER|OBSCN|ENSG00000154358|transcript|ENST00000366709|protein_coding|10/81|c.-5467G>T|||||39761|,T|5_prime_UTR_variant|MODIFIER|OBSCN|ENSG00000154358|transcript|ENST00000366707|protein_coding|10/111|c.-5467G>T|||||39761| GT:AD:AF:DP 0/1:57,1:0.048:58 0/0:14,0:0:14 | |
| chr1 231076123 . G A . t_lod_fstar ClippingRankSum=0;DP=84;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.42;ReadPosRankSum=0.837;TLOD=5.43;ANN=A|upstream_gene_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000519379|retained_intron||n.-3740C>T|||||3740|,A|downstream_gene_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000466507|nonsense_mediated_decay||c.*16173C>T|||||132|,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000366661|protein_coding|7/22|c.789+63C>T||||||,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000366662|protein_coding|5/20|c.630+63C>T||||||,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000414259|protein_coding|5/20|c.630+63C>T||||||,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000481976|nonsense_mediated_decay|5/8|c.630+63C>T||||||,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000522821|protein_coding|4/4|c.478-6516C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TTC13|ENSG00000143643|transcript|ENST00000522399|protein_coding|3/3|c.459+63C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:59,1:0.043:60 0/0:23,0:0:23 | |
| chr1 234743173 . T A . t_lod_fstar ClippingRankSum=0;DP=52;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.52;ReadPosRankSum=-0.133;TLOD=4.55;ANN=A|missense_variant|MODERATE|IRF2BP2|ENSG00000168264|transcript|ENST00000366609|protein_coding|2/2|c.1474A>T|p.Ser492Cys|1505/4663|1474/1764|492/587||,A|missense_variant|MODERATE|IRF2BP2|ENSG00000168264|transcript|ENST00000366610|protein_coding|2/2|c.1426A>T|p.Ser476Cys|1457/4615|1426/1716|476/571||,A|sequence_feature|MODERATE|IRF2BP2|ENSG00000168264|modified-residue:phosphoserine|ENST00000366609|protein_coding|2/2|c.1474A>T||||||,A|sequence_feature|MODERATE|IRF2BP2|ENSG00000168264|modified-residue:phosphoserine|ENST00000366610|protein_coding|2/2|c.1426A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP4-781K5.2|ENSG00000228830|transcript|ENST00000436039|antisense|1/2|n.420T>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|IRF2BP2|ENSG00000168264|transcript|ENST00000491430|processed_transcript|2/2|n.487A>T|||||| GT:AD:AF:DP 0/1:33,1:0.069:34 0/0:18,0:0:18 | |
| chr1 235377278 . TTCC T . t_lod_fstar ClippingRankSum=0;DP=207;ECNT=1;FS=1.653;HCNT=19;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.95;ReadPosRankSum=0.062;TLOD=4.95;ANN=T|disruptive_inframe_deletion|MODERATE|ARID4B|ENSG00000054267|transcript|ENST00000264183|protein_coding|17/24|c.1644_1646delGGA|p.Glu549del|2144/6067|1644/3939|548/1312||,T|disruptive_inframe_deletion|MODERATE|ARID4B|ENSG00000054267|transcript|ENST00000366603|protein_coding|17/24|c.1644_1646delGGA|p.Glu549del|2023/5946|1644/3939|548/1312||,T|disruptive_inframe_deletion|MODERATE|ARID4B|ENSG00000054267|transcript|ENST00000421364|nonsense_mediated_decay|17/25|c.1644_1646delGGA|p.Glu549del|2061/5151|1644/3462|548/1153||,T|upstream_gene_variant|MODIFIER|ARID4B|ENSG00000054267|transcript|ENST00000444620|protein_coding||c.-52_-50delGGA|||||48|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|ARID4B|ENSG00000054267|transcript|ENST00000349213|protein_coding|16/22|c.1583+5827_1583+5829delGGA||||||,T|intron_variant|MODIFIER|ARID4B|ENSG00000054267|transcript|ENST00000491632|retained_intron|16/19|n.2032+5827_2032+5829delGGA||||||,T|non_coding_transcript_exon_variant|MODIFIER|ARID4B|ENSG00000054267|transcript|ENST00000471257|retained_intron|9/12|n.1059_1061delGGA|||||| GT:AD:AF:DP 0/1:106,4:0.025:110 0/0:69,2:0.035:71 | |
| chr1 235872533 . G T . t_lod_fstar ClippingRankSum=0;DP=221;ECNT=1;FS=0;HCNT=40;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.62;ReadPosRankSum=1.054;TLOD=4.46;ANN=T|missense_variant|MODERATE|LYST|ENSG00000143669|transcript|ENST00000389793|protein_coding|44/53|c.10001C>A|p.Pro3334His|10176/13471|10001/11406|3334/3801||,T|missense_variant|MODERATE|LYST|ENSG00000143669|transcript|ENST00000389794|protein_coding|44/53|c.10001C>A|p.Pro3334His|10176/13480|10001/11406|3334/3801||,T|downstream_gene_variant|MODIFIER|LYST|ENSG00000143669|transcript|ENST00000475277|processed_transcript||n.*3876C>A|||||3876|,T|non_coding_transcript_exon_variant|MODIFIER|LYST|ENSG00000143669|transcript|ENST00000473037|processed_transcript|13/22|n.4991C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|LYST|ENSG00000143669|transcript|ENST00000462376|retained_intron|2/2|n.420C>A|||||| GT:AD:AF:DP 0/1:145,7:0.029:152 0/0:67,2:0.022:69 | |
| chr1 236706734 . G C . germline_risk ClippingRankSum=0;DP=27;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.81;ReadPosRankSum=-0.626;TLOD=13.74;ANN=C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000481485|protein_coding||c.*4371G>C|||||4371|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000454943|protein_coding||c.*1743G>C|||||1743|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000430527|protein_coding||c.*1762G>C|||||1762|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000406509|protein_coding||c.*444G>C|||||444|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000532826|retained_intron||n.*4212G>C|||||4212|,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000528782|retained_intron||n.*627G>C|||||627|,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000442397|nonsense_mediated_decay||c.*4521G>C|||||607|,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000434231|nonsense_mediated_decay||c.*4439G>C|||||1728|,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000526652|retained_intron||n.*578G>C|||||578|,C|downstream_gene_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000529796|retained_intron||n.*421G>C|||||421|,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000352231|protein_coding|9/11|c.676-126G>C||||||,C|intron_variant|MODIFIER|RP11-385F5.4|ENSG00000230325|transcript|ENST00000433131|antisense|1/1|n.142-2988C>G||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000527974|protein_coding|8/10|c.676-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000526589|protein_coding|11/13|c.676-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000341872|protein_coding|8/10|c.550-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000450372|protein_coding|9/11|c.676-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000366584|protein_coding|7/9|c.550-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000238181|protein_coding|5/6|c.373-126G>C||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000416919|protein_coding|6/8|c.499-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000323938|protein_coding|7/9|c.469-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000526634|protein_coding|7/9|c.550-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000525042|protein_coding|5/7|c.499-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000528259|retained_intron|3/5|n.522-126G>C||||||,C|intron_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000532640|retained_intron|1/2|n.327-126G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000366583|retained_intron|7/7|n.1372G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000489586|retained_intron|1/3|n.408G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|LGALS8|ENSG00000116977|transcript|ENST00000525789|retained_intron|1/3|n.139G>C|||||| GT:AD:AF:DP 0/1:13,7:0.333:20 0/0:7,0:0:7 | |
| chr1 236740262 . GA G . PASS ClippingRankSum=0;DP=98;ECNT=1;FS=1.031;HCNT=19;MAX_ED=.;MIN_ED=.;MQ=60.11;MQ0=0;MQRankSum=1.878;NLOD=5.70;ReadPosRankSum=-1.429;TLOD=18.08;ANN=G|upstream_gene_variant|MODIFIER|HEATR1|ENSG00000119285|transcript|ENST00000490339|processed_transcript||n.-2188delT|||||2188|,G|intron_variant|MODIFIER|HEATR1|ENSG00000119285|transcript|ENST00000366582|protein_coding|20/44|c.2756-14delT||||||,G|intron_variant|MODIFIER|HEATR1|ENSG00000119285|transcript|ENST00000366581|protein_coding|20/43|c.2756-14delT|||||| GT:AD:AF:DP 0/1:34,19:0.405:53 0/0:34,0:0:34 | |
| chr1 240070836 . C A . PASS ClippingRankSum=0;DP=129;ECNT=1;FS=1.499;HCNT=42;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.03;ReadPosRankSum=-0.591;TLOD=77.83;ANN=A|missense_variant|MODERATE|CHRM3|ENSG00000133019|transcript|ENST00000255380|protein_coding|5/5|c.85C>A|p.Leu29Met|864/8778|85/1773|29/590||,A|missense_variant|MODERATE|CHRM3|ENSG00000133019|transcript|ENST00000448020|protein_coding|3/3|c.85C>A|p.Leu29Met|343/587|85/329|29/108||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:43,42:0.5:85 0/0:44,0:0:44 | |
| chr1 240073139 . G GTA . PASS ClippingRankSum=0;DP=107;ECNT=1;FS=0.761;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60.1;MQ0=0;MQRankSum=1.168;NLOD=6.93;ReadPosRankSum=-0.125;TLOD=90.97;ANN=GTA|3_prime_UTR_variant|MODIFIER|CHRM3|ENSG00000133019|transcript|ENST00000255380|protein_coding|5/5|c.*625_*626dupAT|||||627|INFO_REALIGN_3_PRIME,GTA|downstream_gene_variant|MODIFIER|CHRM3|ENSG00000133019|transcript|ENST00000448020|protein_coding||c.*2059_*2060insTA|||||2060|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:28,44:0.585:72 0/0:30,0:0:30 | |
| chr1 241846828 . CTG C . PASS ClippingRankSum=0;DP=102;ECNT=1;FS=3.492;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=59.71;MQ0=0;MQRankSum=0;NLOD=3.11;ReadPosRankSum=0.164;TLOD=7.99;ANN=C|frameshift_variant|HIGH|WDR64|ENSG00000162843|transcript|ENST00000366552|protein_coding|6/27|c.647_648delTG|p.Val216fs|854/4371|647/3246|216/1081||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|WDR64|ENSG00000162843|transcript|ENST00000468967|nonsense_mediated_decay|6/27|c.647_648delTG|p.Val216fs|854/3735|647/1587|216/528||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|WDR64|ENSG00000162843|transcript|ENST00000437684|protein_coding|6/22|c.647_648delTG|p.Val216fs|854/3870|647/2745|216/914||INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|WDR64|ENSG00000162843|transcript|ENST00000414635|protein_coding||c.-53_-52delTG|||||53|,C|non_coding_transcript_exon_variant|MODIFIER|WDR64|ENSG00000162843|transcript|ENST00000461971|processed_transcript|6/6|n.538_539delTG||||||INFO_REALIGN_3_PRIME;LOF=(WDR64|ENSG00000162843|9|0.33) GT:AD:AF:DP 0/1:63,6:0.08:69 0/0:23,1:0.045:24 | |
| chr1 242159457 . G T . t_lod_fstar ClippingRankSum=0;DP=48;ECNT=1;FS=2.276;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.51;ReadPosRankSum=-1.255;TLOD=5.23;ANN=T|3_prime_UTR_variant|MODIFIER|MAP1LC3C|ENSG00000197769|transcript|ENST00000357246|protein_coding|4/4|c.*8C>A|||||8|,T|downstream_gene_variant|MODIFIER|CFL1P4|ENSG00000213026|transcript|ENST00000451536|processed_pseudogene||n.*2473G>T|||||2473| GT:AD:AF:DP 0/1:23,4:0.087:27 0/0:21,0:0:21 | |
| chr1 243327939 . A C . t_lod_fstar ClippingRankSum=0;DP=302;ECNT=1;FS=11.523;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=57.68;MQ0=11;MQRankSum=-4.932;NLOD=3.23;ReadPosRankSum=-2.893;TLOD=6.02;ANN=C|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366542|protein_coding|13/20|c.3323T>G|p.Leu1108Arg|3375/6828|3323/4755|1108/1584||,C|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366543|protein_coding|12/19|c.3029T>G|p.Leu1010Arg|3352/6727|3029/4383|1010/1460||,C|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366544|protein_coding|12/19|c.3029T>G|p.Leu1010Arg|3352/6805|3029/4461|1010/1486||,C|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000336415|protein_coding|8/15|c.3212T>G|p.Leu1071Arg|3214/5961|3212/4674|1071/1557||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000437499|antisense||n.-1A>C|||||1|,C|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000490813|protein_coding||c.-8328T>G|||||1319|,C|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000413359|protein_coding||c.-143T>G|||||143|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000464936|protein_coding||c.-8328T>G|||||1297|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000492145|protein_coding||c.-8328T>G|||||1327|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000422938|antisense||n.-35A>C|||||35|,C|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000451408|processed_transcript||n.*282T>G|||||282|,C|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000518289|processed_transcript||n.*1352T>G|||||1352|,C|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000522895|protein_coding||c.*4899T>G|||||4803|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:198,6:0.036:204 0/0:79,5:0.079:84 | |
| chr1 243328208 . G A . germline_risk ClippingRankSum=0;DP=236;ECNT=1;FS=15.364;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=49.28;MQ0=38;MQRankSum=-1.318;NLOD=0.691;ReadPosRankSum=-0.393;TLOD=21.50;ANN=A|synonymous_variant|LOW|CEP170|ENSG00000143702|transcript|ENST00000366542|protein_coding|13/20|c.3054C>T|p.Pro1018Pro|3106/6828|3054/4755|1018/1584||,A|synonymous_variant|LOW|CEP170|ENSG00000143702|transcript|ENST00000366543|protein_coding|12/19|c.2760C>T|p.Pro920Pro|3083/6727|2760/4383|920/1460||,A|synonymous_variant|LOW|CEP170|ENSG00000143702|transcript|ENST00000366544|protein_coding|12/19|c.2760C>T|p.Pro920Pro|3083/6805|2760/4461|920/1486||,A|synonymous_variant|LOW|CEP170|ENSG00000143702|transcript|ENST00000336415|protein_coding|8/15|c.2943C>T|p.Pro981Pro|2945/5961|2943/4674|981/1557||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000490813|protein_coding||c.-8597C>T|||||1588|,A|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000413359|protein_coding||c.-412C>T|||||412|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000464936|protein_coding||c.-8597C>T|||||1566|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000492145|protein_coding||c.-8597C>T|||||1596|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000451408|processed_transcript||n.*13C>T|||||13|,A|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000518289|processed_transcript||n.*1083C>T|||||1083|,A|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000522895|protein_coding||c.*4630C>T|||||4534|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000461671|nonsense_mediated_decay||c.*11869C>T|||||4788|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000437499|antisense|1/2|n.29+240G>A||||||,A|intron_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000422938|antisense|1/1|n.115+120G>A|||||| GT:AD:AF:DP 0/1:102,12:0.133:114 0/0:59,19:0.237:78 | |
| chr1 243329211 . G T . PASS ClippingRankSum=0;DP=358;ECNT=1;FS=1.957;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=54.5;MQ0=52;MQRankSum=-3.726;NLOD=12.70;ReadPosRankSum=-0.903;TLOD=11.78;ANN=T|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366542|protein_coding|13/20|c.2051C>A|p.Thr684Lys|2103/6828|2051/4755|684/1584||,T|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366543|protein_coding|12/19|c.1757C>A|p.Thr586Lys|2080/6727|1757/4383|586/1460||,T|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000366544|protein_coding|12/19|c.1757C>A|p.Thr586Lys|2080/6805|1757/4461|586/1486||,T|missense_variant|MODERATE|CEP170|ENSG00000143702|transcript|ENST00000336415|protein_coding|8/15|c.1940C>A|p.Thr647Lys|1942/5961|1940/4674|647/1557||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000490813|protein_coding||c.-9600C>A|||||2591|,T|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000413359|protein_coding||c.-1415C>A|||||1415|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000464936|protein_coding||c.-9600C>A|||||2569|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000492145|protein_coding||c.-9600C>A|||||2599|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000518289|processed_transcript||n.*80C>A|||||80|,T|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000522895|protein_coding||c.*3627C>A|||||3531|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000461671|nonsense_mediated_decay||c.*10866C>A|||||3785|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000437499|antisense|1/2|n.29+1243G>T||||||,T|intron_variant|MODIFIER|RP11-261C10.4|ENSG00000232085|transcript|ENST00000422938|antisense|1/1|n.115+1123G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|CEP170|ENSG00000143702|transcript|ENST00000451408|processed_transcript|2/2|n.254C>A|||||| GT:AD:AF:DP 0/1:198,7:0.048:205 0/0:87,12:0.123:99 | |
| chr1 243666519 . C T . PASS ClippingRankSum=0;DP=409;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=20.40;ReadPosRankSum=-0.061;TLOD=6.86;ANN=T|3_prime_UTR_variant|MODIFIER|AKT3|ENSG00000117020|transcript|ENST00000263826|protein_coding|13/13|c.*2032G>A|||||2032|,T|3_prime_UTR_variant|MODIFIER|AKT3|ENSG00000117020|transcript|ENST00000366539|protein_coding|14/14|c.*2032G>A|||||2032|,T|downstream_gene_variant|MODIFIER|SDCCAG8|ENSG00000054282|transcript|ENST00000366541|protein_coding||c.*3432C>T|||||3125|,T|downstream_gene_variant|MODIFIER|SDCCAG8|ENSG00000054282|transcript|ENST00000355875|protein_coding||c.*3432C>T|||||3131|,T|downstream_gene_variant|MODIFIER|SDCCAG8|ENSG00000054282|transcript|ENST00000343783|protein_coding||c.*3432C>T|||||3127|,T|downstream_gene_variant|MODIFIER|SDCCAG8|ENSG00000054282|transcript|ENST00000435549|protein_coding||c.*3432C>T|||||3126|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|SDCCAG8|ENSG00000054282|transcript|ENST00000497459|processed_transcript||n.*3128C>T|||||3128|,T|intron_variant|MODIFIER|AKT3|ENSG00000117020|transcript|ENST00000336199|protein_coding|12/13|c.1355-3431G>A||||||,T|intron_variant|MODIFIER|AKT3|ENSG00000117020|transcript|ENST00000366540|protein_coding|13/13|c.1355-3431G>A|||||| GT:AD:AF:DP 0/1:303,7:0.024:310 0/0:98,0:0:98 | |
| chr1 244571936 . CT C . PASS ClippingRankSum=0;DP=369;ECNT=1;FS=0.419;HCNT=25;MAX_ED=.;MIN_ED=.;MQ=60.15;MQ0=0;MQRankSum=2.846;NLOD=10.31;ReadPosRankSum=-3.142;TLOD=59.74;ANN=C|3_prime_UTR_variant|MODIFIER|ADSS|ENSG00000035687|transcript|ENST00000366535|protein_coding|13/13|c.*951delA|||||951|,C|downstream_gene_variant|MODIFIER|ADSS|ENSG00000035687|transcript|ENST00000468215|processed_transcript||n.*2732delA|||||2732|,C|intron_variant|MODIFIER|RP11-518L10.5|ENSG00000240963|transcript|ENST00000417765|antisense|2/3|n.157+77delA|||||| GT:AD:AF:DP 0/1:121,122:0.479:243 0/0:84,4:0.051:88 | |
| chr1 244715954 . T G . t_lod_fstar ClippingRankSum=0;DP=50;ECNT=1;FS=2.759;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.52;ReadPosRankSum=-0.398;TLOD=4.22;ANN=G|missense_variant|MODERATE|C1orf101|ENSG00000179397|transcript|ENST00000366534|protein_coding|9/22|c.867T>G|p.His289Gln|921/3333|867/2856|289/951||,G|missense_variant|MODERATE|C1orf101|ENSG00000179397|transcript|ENST00000366533|protein_coding|9/21|c.867T>G|p.His289Gln|909/3019|867/2499|289/832||,G|missense_variant|MODERATE|C1orf101|ENSG00000179397|transcript|ENST00000366531|protein_coding|6/19|c.414T>G|p.His138Gln|734/3000|414/2403|138/800||,G|missense_variant|MODERATE|C1orf101|ENSG00000179397|transcript|ENST00000428042|protein_coding|5/18|c.627T>G|p.His209Gln|627/2895|627/2616|209/871||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|C1orf101|ENSG00000179397|transcript|ENST00000478554|processed_transcript||n.*177T>G|||||177|,G|downstream_gene_variant|MODIFIER|C1orf101|ENSG00000179397|transcript|ENST00000464170|processed_transcript||n.*187T>G|||||187|,G|intron_variant|MODIFIER|C1orf101|ENSG00000179397|transcript|ENST00000473875|processed_transcript|6/15|n.576-8016T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|C1orf101|ENSG00000179397|transcript|ENST00000460986|processed_transcript|6/6|n.711T>G|||||| GT:AD:AF:DP 0/1:32,2:0.067:34 0/0:16,0:0:16 | |
| chr1 247014728 . T C . t_lod_fstar ClippingRankSum=0;DP=272;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=59.6;MQ0=0;MQRankSum=-1.037;NLOD=15.95;ReadPosRankSum=-0.343;TLOD=4.02;ANN=C|missense_variant|MODERATE|AHCTF1|ENSG00000153207|transcript|ENST00000366508|protein_coding|33/36|c.4685A>G|p.Lys1562Arg|4822/8751|4685/6906|1562/2301||,C|missense_variant|MODERATE|AHCTF1|ENSG00000153207|transcript|ENST00000326225|protein_coding|33/36|c.4607A>G|p.Lys1536Arg|4704/8633|4607/6828|1536/2275||,C|missense_variant|MODERATE|AHCTF1|ENSG00000153207|transcript|ENST00000391829|protein_coding|33/36|c.4580A>G|p.Lys1527Arg|4704/8629|4580/6801|1527/2266||,C|upstream_gene_variant|MODIFIER|AHCTF1|ENSG00000153207|transcript|ENST00000498601|nonsense_mediated_decay||c.-1577A>G|||||1577|WARNING_TRANSCRIPT_NO_START_CODON,C|non_coding_transcript_exon_variant|MODIFIER|AHCTF1|ENSG00000153207|transcript|ENST00000470300|processed_transcript|24/26|n.3195A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AHCTF1|ENSG00000153207|transcript|ENST00000483900|processed_transcript|12/12|n.1896A>G|||||| GT:AD:AF:DP 0/1:201,4:0.021:205 0/0:67,0:0:67 | |
| chr1 248247237 . C A . germline_risk ClippingRankSum=0;DP=373;ECNT=1;FS=45.934;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=45.48;MQ0=20;MQRankSum=-3.914;NLOD=1.61;ReadPosRankSum=0.187;TLOD=41.84;ANN=A|intron_variant|MODIFIER|OR2L13|ENSG00000196071|transcript|ENST00000366478|protein_coding|1/2|c.-143-14716C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|OR2T32P|ENSG00000197067|transcript|ENST00000403423|unprocessed_pseudogene|1/1|n.662G>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|OR2T32P|ENSG00000197067|transcript|ENST00000356294|pseudogene|2/2|n.658G>T|||||| GT:AD:AF:DP 0/1:203,28:0.138:231 0/0:89,11:0.13:100 | |
| chr1 248247745 . GC G . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=285;ECNT=2;FS=4.72;HCNT=26;MAX_ED=2;MIN_ED=2;MQ=58.77;MQ0=1;MQRankSum=-13.756;NLOD=13.26;ReadPosRankSum=-2.691;TLOD=22.64;ANN=G|splice_acceptor_variant&splice_region_variant&intron_variant|HIGH|OR2T32P|ENSG00000197067|transcript|ENST00000356294|pseudogene|1/1|n.151-2delG||||||,G|intron_variant|MODIFIER|OR2L13|ENSG00000196071|transcript|ENST00000366478|protein_coding|1/2|c.-143-14206delC||||||INFO_REALIGN_3_PRIME,G|non_coding_transcript_exon_variant|MODIFIER|OR2T32P|ENSG00000197067|transcript|ENST00000403423|unprocessed_pseudogene|1/1|n.153delG|||||| GT:AD:AF:DP:PGT:PID 0/1:187,9:0.058:196:0|1:248247745_GC_G 0/0:76,1:0.018:77:0|1:248247745_GC_G | |
| chr1 248247747 . C T . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=281;ECNT=2;FS=4.734;HCNT=26;MAX_ED=2;MIN_ED=2;MQ=58.76;MQ0=1;MQRankSum=-13.859;NLOD=13.26;ReadPosRankSum=-2.9;TLOD=22.49;ANN=T|splice_donor_variant&splice_region_variant&intron_variant|HIGH|OR2T32P|ENSG00000197067|transcript|ENST00000356294|pseudogene|1/1|n.150+2G>A||||||,T|intron_variant|MODIFIER|OR2L13|ENSG00000196071|transcript|ENST00000366478|protein_coding|1/2|c.-143-14206C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|OR2T32P|ENSG00000197067|transcript|ENST00000403423|unprocessed_pseudogene|1/1|n.152G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:186,9:0.054:195:0|1:248247745_GC_G 0/0:77,1:0.017:78:0|1:248247745_GC_G | |
| chr1 248436313 . A G . PASS ClippingRankSum=0;DP=308;ECNT=1;FS=21.951;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=55.57;MQ0=33;MQRankSum=-3.126;NLOD=2.43;ReadPosRankSum=-1.267;TLOD=6.88;ANN=G|synonymous_variant|LOW|OR2T33|ENSG00000177212|transcript|ENST00000318021|protein_coding|1/1|c.804T>C|p.His268His|826/1066|804/963|268/320|| GT:AD:AF:DP 0/1:169,8:0.055:177 0/0:79,18:0.176:97 | |
| chr1 248605183 . C G . PASS ClippingRankSum=0;DP=142;ECNT=1;FS=16.133;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=53.18;MQ0=4;MQRankSum=-4.315;NLOD=7.82;ReadPosRankSum=-1.095;TLOD=10.50;ANN=G|missense_variant|MODERATE|OR2T7|ENSG00000227152|transcript|ENST00000460972|protein_coding|1/1|c.676C>G|p.Arg226Gly|676/927|676/927|226/308|| GT:AD:AF:DP 0/1:90,7:0.088:97 0/0:36,1:0.037:37 | |
| chr1 248617028 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=124;ECNT=3;FS=0;HCNT=2;MAX_ED=26;MIN_ED=23;MQ=44.54;MQ0=35;MQRankSum=0.01;NLOD=0.617;ReadPosRankSum=-2.067;TLOD=5.63;ANN=C|synonymous_variant|LOW|OR2T2|ENSG00000196240|transcript|ENST00000342927|protein_coding|1/1|c.930T>C|p.Gly310Gly|952/1054|930/975|310/324|| GT:AD:AF:DP:PGT:PID 0/1:52,2:0.054:54:0|1:248617028_T_C 0/0:24,4:0.174:28:0|1:248617028_T_C | |
| chr1 248617051 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=106;ECNT=3;FS=1.977;HCNT=2;MAX_ED=26;MIN_ED=23;MQ=46.22;MQ0=22;MQRankSum=-0.749;NLOD=0.617;ReadPosRankSum=-2.222;TLOD=5.62;ANN=T|missense_variant|MODERATE|OR2T2|ENSG00000196240|transcript|ENST00000342927|protein_coding|1/1|c.953C>T|p.Ala318Val|975/1054|953/975|318/324|| GT:AD:AF:DP:PGT:PID 0/1:52,2:0.054:54:0|1:248617028_T_C 0/0:20,2:0.105:22:0|1:248617028_T_C | |
| chr1 248617054 . C CTG . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=106;ECNT=3;FS=1.958;HCNT=2;MAX_ED=26;MIN_ED=23;MQ=46.57;MQ0=22;MQRankSum=-0.767;NLOD=0.617;ReadPosRankSum=-2.17;TLOD=5.65;ANN=CTG|frameshift_variant&stop_gained|HIGH|OR2T2|ENSG00000196240|transcript|ENST00000342927|protein_coding|1/1|c.959_960dupTG|p.Ile321fs|983/1054|961/975|321/324||INFO_REALIGN_3_PRIME GT:AD:AF:DP:PGT:PID 0/1:52,2:0.056:54:0|1:248617028_T_C 0/0:21,2:0.111:23:0|1:248617028_T_C | |
| chr1 248722739 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=357;ECNT=5;FS=24.044;HCNT=42;MAX_ED=49;MIN_ED=13;MQ=43.21;MQ0=101;MQRankSum=-3.901;NLOD=10.85;ReadPosRankSum=-0.064;TLOD=44.83;ANN=C|synonymous_variant|LOW|OR2T29|ENSG00000182783|transcript|ENST00000328570|protein_coding|1/1|c.54C>G|p.Leu18Leu|59/1014|54/948|18/315||,C|upstream_gene_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000436515|antisense||n.-3162G>C|||||3162|,C|intron_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000438623|antisense|1/1|n.92-3162G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:110,25:0.146:135:0|1:248722739_G_C 0/0:109,1:0.012:110:0|1:248722739_G_C | |
| chr1 248722752 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=379;ECNT=5;FS=22.138;HCNT=42;MAX_ED=49;MIN_ED=13;MQ=44.44;MQ0=104;MQRankSum=-3.649;NLOD=12.36;ReadPosRankSum=-0.665;TLOD=39.79;ANN=G|missense_variant|MODERATE|OR2T29|ENSG00000182783|transcript|ENST00000328570|protein_coding|1/1|c.41T>C|p.Leu14Ser|46/1014|41/948|14/315||,G|upstream_gene_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000436515|antisense||n.-3149A>G|||||3149|,G|intron_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000438623|antisense|1/1|n.92-3149A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:127,18:0.121:145:0|1:248722739_G_C 0/0:119,1:0.011:120:0|1:248722739_G_C | |
| chr1 248722756 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=381;ECNT=5;FS=18.628;HCNT=42;MAX_ED=49;MIN_ED=13;MQ=44.64;MQ0=104;MQRankSum=-3.322;NLOD=12.66;ReadPosRankSum=-0.356;TLOD=30.33;ANN=A|missense_variant|MODERATE|OR2T29|ENSG00000182783|transcript|ENST00000328570|protein_coding|1/1|c.37A>T|p.Arg13Trp|42/1014|37/948|13/315||,A|upstream_gene_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000436515|antisense||n.-3145T>A|||||3145|,A|intron_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000438623|antisense|1/1|n.92-3145T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:130,15:0.088:145:0|1:248722739_G_C 0/0:122,1:0.011:123:0|1:248722739_G_C | |
| chr1 248722767 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=403;ECNT=5;FS=19.955;HCNT=42;MAX_ED=49;MIN_ED=13;MQ=45.51;MQ0=95;MQRankSum=-2.441;NLOD=16.57;ReadPosRankSum=-1.471;TLOD=29.87;ANN=C|missense_variant|MODERATE|OR2T29|ENSG00000182783|transcript|ENST00000328570|protein_coding|1/1|c.26A>G|p.Asn9Ser|31/1014|26/948|9/315||,C|sequence_feature|MODERATE|OR2T29|ENSG00000182783|glycosylation-site:N-linked_(GlcNAc...)|ENST00000328570|protein_coding|1/1|c.26A>G||||||,C|upstream_gene_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000436515|antisense||n.-3134T>C|||||3134|,C|intron_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000438623|antisense|1/1|n.92-3134T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:153,13:0.08:166:0|1:248722739_G_C 0/0:132,1:0.009615:133:0|1:248722739_G_C | |
| chr1 248722788 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=440;ECNT=5;FS=18.299;HCNT=46;MAX_ED=49;MIN_ED=13;MQ=46.75;MQ0=73;MQRankSum=-1.314;NLOD=21.36;ReadPosRankSum=-1.091;TLOD=28.31;ANN=T|missense_variant|MODERATE|OR2T29|ENSG00000182783|transcript|ENST00000328570|protein_coding|1/1|c.5C>A|p.Ala2Asp|10/1014|5/948|2/315||,T|upstream_gene_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000436515|antisense||n.-3113G>T|||||3113|,T|intron_variant|MODIFIER|RP11-438F14.3|ENSG00000224521|transcript|ENST00000438623|antisense|1/1|n.92-3113G>T|||||| GT:AD:AF:DP 0/1:198,11:0.072:209 0/0:148,1:0.009804:149 | |
| chr2 1796204 . G A . PASS ClippingRankSum=0;DP=69;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.32;ReadPosRankSum=0.665;TLOD=6.50;ANN=A|synonymous_variant|LOW|MYT1L|ENSG00000186487|transcript|ENST00000399161|protein_coding|24/25|c.3309C>T|p.Ile1103Ile|4057/7063|3309/3561|1103/1186||,A|synonymous_variant|LOW|MYT1L|ENSG00000186487|transcript|ENST00000407844|protein_coding|6/7|c.303C>T|p.Ile101Ile|659/3642|303/555|101/184||,A|synonymous_variant|LOW|MYT1L|ENSG00000186487|transcript|ENST00000399157|protein_coding|5/6|c.471C>T|p.Ile157Ile|471/670|471/609|157/202||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|MYT1L|ENSG00000186487|transcript|ENST00000428368|protein_coding|24/25|c.3303C>T|p.Ile1101Ile|3973/4850|3303/3555|1101/1184|| GT:AD:AF:DP 0/1:38,4:0.1:42 0/0:27,0:0:27 | |
| chr2 8823841 . CACA C . PASS ClippingRankSum=0;DP=198;ECNT=1;FS=1.474;HCNT=43;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.33;ReadPosRankSum=1.232;TLOD=17.58;ANN=C|3_prime_UTR_variant|MODIFIER|ID2|ENSG00000115738|transcript|ENST00000234091|protein_coding|5/5|c.*51_*53delCAA|||||829|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|ID2|ENSG00000115738|transcript|ENST00000396290|protein_coding|3/3|c.*51_*53delCAA|||||829|INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|AC011747.7|ENSG00000235092|transcript|ENST00000455965|antisense||n.-1851_-1849delTGT|||||1849|,C|upstream_gene_variant|MODIFIER|AC011747.7|ENSG00000235092|transcript|ENST00000433340|antisense||n.-4903_-4901delTGT|||||4901|,C|upstream_gene_variant|MODIFIER|AC011747.7|ENSG00000235092|transcript|ENST00000421298|antisense||n.-4658_-4656delTGT|||||4656|,C|upstream_gene_variant|MODIFIER|AC011747.7|ENSG00000235092|transcript|ENST00000418957|antisense||n.-4861_-4859delTGT|||||4859|,C|downstream_gene_variant|MODIFIER|ID2|ENSG00000115738|transcript|ENST00000331129|protein_coding||c.*813_*815delACA|||||705|,C|non_coding_transcript_exon_variant|MODIFIER|ID2|ENSG00000115738|transcript|ENST00000472142|retained_intron|2/2|n.171_173delCAA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:107,8:0.071:115 0/0:73,0:0:73 | |
| chr2 9475200 . TTG T . t_lod_fstar ClippingRankSum=0;DP=208;ECNT=1;FS=4.338;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60.05;MQ0=0;MQRankSum=6.116;NLOD=11.40;ReadPosRankSum=0.353;TLOD=4.38;ANN=T|intron_variant|MODIFIER|ASAP2|ENSG00000151693|transcript|ENST00000281419|protein_coding|8/27|c.763-10_763-9delGT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|ASAP2|ENSG00000151693|transcript|ENST00000315273|protein_coding|8/26|c.763-10_763-9delGT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:133,5:0.031:138 0/0:52,0:0:52 | |
| chr2 9616148 . G T . t_lod_fstar ClippingRankSum=0;DP=174;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.23;ReadPosRankSum=-0.337;TLOD=4.18;ANN=T|synonymous_variant|LOW|IAH1|ENSG00000134330|transcript|ENST00000497473|protein_coding|2/6|c.114G>T|p.Ser38Ser|151/1266|114/747|38/248||,T|synonymous_variant|LOW|IAH1|ENSG00000134330|transcript|ENST00000351760|nonsense_mediated_decay|2/6|c.102G>T|p.Ser34Ser|103/837|102/225|34/74||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|IAH1|ENSG00000134330|transcript|ENST00000481688|protein_coding|2/6|c.39G>T|p.Ser13Ser|393/1011|39/480|13/159||WARNING_TRANSCRIPT_NO_STOP_CODON,T|5_prime_UTR_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000482918|protein_coding|2/6|c.-226G>T|||||5323|,T|upstream_gene_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000487850|processed_transcript||n.-4852G>T|||||4852|,T|downstream_gene_variant|MODIFIER|CPSF3|ENSG00000119203|transcript|ENST00000238112|protein_coding||c.*3002G>T|||||2918|,T|downstream_gene_variant|MODIFIER|CPSF3|ENSG00000119203|transcript|ENST00000460593|protein_coding||c.*3002G>T|||||2927|,T|downstream_gene_variant|MODIFIER|CPSF3|ENSG00000119203|transcript|ENST00000489403|processed_transcript||n.*2921G>T|||||2921|,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000496603|protein_coding|1/3|c.-206+2120G>T||||||WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000470914|protein_coding|1/4|c.-206+1372G>T||||||,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000492223|nonsense_mediated_decay|1/4|c.81+1372G>T||||||,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000495050|retained_intron|1/3|n.84+1372G>T||||||,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000481367|protein_coding|1/6|c.71+1372G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000545602|protein_coding|1/6|c.-206+1372G>T||||||,T|intron_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000495797|protein_coding|1/3|c.-174+802G>T||||||WARNING_TRANSCRIPT_INCOMPLETE,T|non_coding_transcript_exon_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000489468|processed_transcript|2/7|n.159G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|IAH1|ENSG00000134330|transcript|ENST00000495494|processed_transcript|1/4|n.346G>T|||||| GT:AD:AF:DP 0/1:111,4:0.027:115 0/0:59,0:0:59 | |
| chr2 10917818 . CAG C . PASS ClippingRankSum=0;DP=106;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.00;ReadPosRankSum=0.89;TLOD=11.36;ANN=C|frameshift_variant|HIGH|ATP6V1C2|ENSG00000143882|transcript|ENST00000272238|protein_coding|11/14|c.946_947delAG|p.Ser316fs|1055/1565|946/1284|316/427||INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|ATP6V1C2|ENSG00000143882|transcript|ENST00000480289|retained_intron||n.-795_-794delAG|||||795|,C|intron_variant|MODIFIER|ATP6V1C2|ENSG00000143882|transcript|ENST00000381661|protein_coding|10/12|c.826-867_826-866delAG||||||INFO_REALIGN_3_PRIME;LOF=(ATP6V1C2|ENSG00000143882|3|0.33) GT:AD:AF:DP 0/1:52,8:0.143:60 0/0:29,0:0:29 | |
| chr2 11731475 . G T . t_lod_fstar ClippingRankSum=0;DP=191;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.83;ReadPosRankSum=-0.908;TLOD=4.18;ANN=T|downstream_gene_variant|MODIFIER|GREB1|ENSG00000196208|transcript|ENST00000263834|protein_coding||c.*3897G>T|||||3106|,T|intron_variant|MODIFIER|GREB1|ENSG00000196208|transcript|ENST00000234142|protein_coding|9/31|c.1346-1427G>T||||||,T|intron_variant|MODIFIER|GREB1|ENSG00000196208|transcript|ENST00000381486|protein_coding|10/32|c.1346-1427G>T||||||,T|intron_variant|MODIFIER|GREB1|ENSG00000196208|transcript|ENST00000381483|protein_coding|10/10|c.1346-47G>T||||||,T|intron_variant|MODIFIER|GREB1|ENSG00000196208|transcript|ENST00000432985|protein_coding|1/8|c.248-1427G>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:136,5:0.032:141 0/0:50,0:0:50 | |
| chr2 13555027 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=250;ECNT=2;FS=1.027;HCNT=43;MAX_ED=51;MIN_ED=51;MQ=58.22;MQ0=2;MQRankSum=-13.757;NLOD=11.87;ReadPosRankSum=1.007;TLOD=10.95;ANN=T|intergenic_region|MODIFIER|AC064875.2-AC092635.1|ENSG00000225649-ENSG00000229370|intergenic_region|ENSG00000225649-ENSG00000229370|||n.13555027G>T|||||| GT:AD:AF:DP 0/1:155,12:0.065:167 0/0:73,2:0.02:75 | |
| chr2 13555078 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=191;ECNT=2;FS=1.086;HCNT=35;MAX_ED=51;MIN_ED=51;MQ=57.67;MQ0=2;MQRankSum=-12.368;NLOD=6.65;ReadPosRankSum=1.648;TLOD=12.15;ANN=C|intergenic_region|MODIFIER|AC064875.2-AC092635.1|ENSG00000225649-ENSG00000229370|intergenic_region|ENSG00000225649-ENSG00000229370|||n.13555078A>C|||||| GT:AD:AF:DP 0/1:118,12:0.077:130 0/0:50,2:0.029:52 | |
| chr2 15696946 . G T . t_lod_fstar ClippingRankSum=0;DP=387;ECNT=1;FS=1.609;HCNT=23;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=20.96;ReadPosRankSum=-1.001;TLOD=4.03;ANN=T|splice_region_variant&intron_variant|LOW|NBAS|ENSG00000151779|transcript|ENST00000281513|protein_coding|2/51|c.173-3C>A||||||,T|splice_region_variant&intron_variant|LOW|NBAS|ENSG00000151779|transcript|ENST00000441750|protein_coding|2/49|c.173-3C>A|||||| GT:AD:AF:DP 0/1:272,5:0.017:277 0/0:109,1:0.014:110 | |
| chr2 15746047 . ATC A . t_lod_fstar ClippingRankSum=0;DP=68;ECNT=1;FS=4.34;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.71;ReadPosRankSum=-0.092;TLOD=5.99;ANN=A|intron_variant|MODIFIER|DDX1|ENSG00000079785|transcript|ENST00000233084|protein_coding|10/25|c.626-13_626-12delCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|DDX1|ENSG00000079785|transcript|ENST00000381341|protein_coding|11/26|c.626-13_626-12delCT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:38,6:0.1:44 0/0:23,0:0:23 | |
| chr2 17962195 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=183;ECNT=9;FS=14.914;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.633;ReadPosRankSum=1.226;TLOD=7.64;ANN=T|synonymous_variant|LOW|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1716C>T|p.Thr572Thr|1841/5722|1716/2727|572/908||,T|synonymous_variant|LOW|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1716C>T|p.Thr572Thr|1930/6367|1716/2727|572/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*158C>T|||||158|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6887G>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6887G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:139,4:0.03:143:0|1:17962195_C_T 0/0:37,2:0.063:39:0|1:17962195_C_T | |
| chr2 17962197 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=179;ECNT=9;FS=14.769;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.633;ReadPosRankSum=1.02;TLOD=7.60;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1718C>T|p.Ser573Leu|1843/5722|1718/2727|573/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1718C>T|p.Ser573Leu|1932/6367|1718/2727|573/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*160C>T|||||160|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6885G>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6885G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:135,4:0.029:139:0|1:17962195_C_T 0/0:37,2:0.063:39:0|1:17962195_C_T | |
| chr2 17962198 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=179;ECNT=9;FS=14.625;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.633;ReadPosRankSum=1.004;TLOD=7.62;ANN=T|synonymous_variant|LOW|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1719A>T|p.Ser573Ser|1844/5722|1719/2727|573/908||,T|synonymous_variant|LOW|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1719A>T|p.Ser573Ser|1933/6367|1719/2727|573/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*161A>T|||||161|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6884T>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6884T>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:135,4:0.029:139:0|1:17962195_C_T 0/0:37,2:0.063:39:0|1:17962195_C_T | |
| chr2 17962200 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=175;ECNT=9;FS=14.748;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.934;ReadPosRankSum=0.825;TLOD=7.65;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1721C>T|p.Ser574Phe|1846/5722|1721/2727|574/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1721C>T|p.Ser574Phe|1935/6367|1721/2727|574/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*163C>T|||||163|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6882G>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6882G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:131,4:0.03:135:0|1:17962195_C_T 0/0:37,2:0.061:39:0|1:17962195_C_T | |
| chr2 17962202 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=175;ECNT=9;FS=14.885;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.23;ReadPosRankSum=0.784;TLOD=7.69;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1723C>T|p.His575Tyr|1848/5722|1723/2727|575/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1723C>T|p.His575Tyr|1937/6367|1723/2727|575/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*165C>T|||||165|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6880G>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6880G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:131,4:0.031:135:0|1:17962195_C_T 0/0:37,2:0.059:39:0|1:17962195_C_T | |
| chr2 17962205 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=176;ECNT=9;FS=14.823;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.23;ReadPosRankSum=0.565;TLOD=7.72;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1726A>T|p.Asn576Tyr|1851/5722|1726/2727|576/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1726A>T|p.Asn576Tyr|1940/6367|1726/2727|576/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*168A>T|||||168|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6877T>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6877T>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:133,4:0.032:137:0|1:17962195_C_T 0/0:36,2:0.059:38:0|1:17962195_C_T | |
| chr2 17962206 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=174;ECNT=9;FS=14.814;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.23;ReadPosRankSum=0.392;TLOD=7.70;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1727A>T|p.Asn576Ile|1852/5722|1727/2727|576/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1727A>T|p.Asn576Ile|1941/6367|1727/2727|576/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*169A>T|||||169|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6876T>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6876T>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:131,4:0.031:135:0|1:17962195_C_T 0/0:36,2:0.059:38:0|1:17962195_C_T | |
| chr2 17962208 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=170;ECNT=9;FS=14.932;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.633;ReadPosRankSum=0.187;TLOD=7.72;ANN=T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1729A>T|p.Ile577Leu|1854/5722|1729/2727|577/908||,T|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1729A>T|p.Ile577Leu|1943/6367|1729/2727|577/908||,T|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*171A>T|||||171|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6874T>A||||||,T|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6874T>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:127,4:0.032:131:0|1:17962195_C_T 0/0:36,2:0.063:38:0|1:17962195_C_T | |
| chr2 17962212 . C G . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=166;ECNT=9;FS=14.981;HCNT=24;MAX_ED=17;MIN_ED=2;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.632;ReadPosRankSum=-0.114;TLOD=7.80;ANN=G|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000317402|protein_coding|14/14|c.1733C>G|p.Ser578Cys|1858/5722|1733/2727|578/908||,G|missense_variant|MODERATE|GEN1|ENSG00000178295|transcript|ENST00000381254|protein_coding|14/14|c.1733C>G|p.Ser578Cys|1947/6367|1733/2727|578/908||,G|downstream_gene_variant|MODIFIER|GEN1|ENSG00000178295|transcript|ENST00000528873|protein_coding||c.*175C>G|||||175|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000402989|protein_coding|4/29|c.-6+6870G>C||||||,G|intron_variant|MODIFIER|SMC6|ENSG00000163029|transcript|ENST00000428868|protein_coding|3/4|c.-6+6870G>C||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:124,4:0.034:128:0|1:17962195_C_T 0/0:34,2:0.063:36:0|1:17962195_C_T | |
| chr2 20482976 . AGCT A . t_lod_fstar ClippingRankSum=0;DP=273;ECNT=1;FS=2.105;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.94;ReadPosRankSum=0.307;TLOD=4.63;ANN=A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000361078|protein_coding|11/20|c.1449_1451delAGC|p.Ala484del|1474/6117|1449/3201|483/1066||,A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000338086|protein_coding|11/20|c.1449_1451delAGC|p.Ala484del|1474/6112|1449/3195|483/1064||,A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000319801|protein_coding|11/19|c.1449_1451delAGC|p.Ala484del|1474/5880|1449/2964|483/987||,A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000440577|protein_coding|9/17|c.1122_1124delAGC|p.Ala375del|1124/4352|1122/2631|374/876||WARNING_TRANSCRIPT_NO_START_CODON,A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000536417|protein_coding|11/20|c.1281_1283delAGC|p.Ala428del|1385/3404|1281/3027|427/1008||,A|disruptive_inframe_deletion|MODERATE|PUM2|ENSG00000055917|transcript|ENST00000403432|protein_coding|12/21|c.1449_1451delAGC|p.Ala484del|1575/3594|1449/3195|483/1064|| GT:AD:AF:DP 0/1:169,3:0.018:172 0/0:73,0:0:73 | |
| chr2 21236242 . G T . t_lod_fstar ClippingRankSum=0;DP=179;ECNT=1;FS=4.741;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.73;ReadPosRankSum=1.55;TLOD=5.17;ANN=T|missense_variant|MODERATE|APOB|ENSG00000084674|transcript|ENST00000233242|protein_coding|25/29|c.4006C>A|p.Gln1336Lys|4134/14121|4006/13692|1336/4563|| GT:AD:AF:DP 0/1:119,4:0.032:123 0/0:55,0:0:55 | |
| chr2 21263769 . GAC G . t_lod_fstar ClippingRankSum=0;DP=112;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.13;ReadPosRankSum=-1.821;TLOD=4.05;ANN=G|intron_variant|MODIFIER|APOB|ENSG00000084674|transcript|ENST00000233242|protein_coding|4/28|c.383+39_383+40delGT||||||,G|intron_variant|MODIFIER|APOB|ENSG00000084674|transcript|ENST00000399256|protein_coding|4/16|c.383+39_383+40delGT|||||| GT:AD:AF:DP 0/1:70,3:0.04:73 0/0:38,0:0:38 | |
| chr2 23608448 . CGGA C . t_lod_fstar ClippingRankSum=0;DP=121;ECNT=1;FS=3.987;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60.09;MQ0=0;MQRankSum=4.416;NLOD=4.02;ReadPosRankSum=-0.937;TLOD=5.52;ANN=C|5_prime_UTR_variant|MODIFIER|KLHL29|ENSG00000119771|transcript|ENST00000486442|protein_coding|1/14|c.-344_-342delGGA|||||176604|INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|AC012506.4|ENSG00000235497|transcript|ENST00000430051|lincRNA||n.-4325_-4323delTCC|||||4323|,C|upstream_gene_variant|MODIFIER|AC012506.4|ENSG00000235497|transcript|ENST00000421563|lincRNA||n.-4281_-4279delTCC|||||4279| GT:AD:AF:DP 0/1:78,4:0.057:82 0/0:37,2:0.069:39 | |
| chr2 24471620 . C T . PASS ClippingRankSum=0;DP=117;ECNT=1;FS=0.925;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.52;ReadPosRankSum=-0.417;TLOD=34.90;ANN=T|splice_acceptor_variant&intron_variant|HIGH|ITSN2|ENSG00000198399|transcript|ENST00000355123|protein_coding|26/39|c.3167-1G>A||||||,T|splice_acceptor_variant&intron_variant|HIGH|ITSN2|ENSG00000198399|transcript|ENST00000361999|protein_coding|25/38|c.3086-1G>A||||||,T|splice_acceptor_variant&intron_variant|HIGH|ITSN2|ENSG00000198399|transcript|ENST00000406921|protein_coding|26/29|c.3167-1G>A||||||,T|sequence_feature|LOW|ITSN2|ENSG00000198399|beta-strand:combinatorial_evidence_used_in_manual_assertion|ENST00000355123|protein_coding||c.3167-1G>A||||||,T|sequence_feature|LOW|ITSN2|ENSG00000198399|beta-strand:combinatorial_evidence_used_in_manual_assertion|ENST00000361999|protein_coding||c.3086-1G>A||||||,T|sequence_feature|LOW|ITSN2|ENSG00000198399|beta-strand:combinatorial_evidence_used_in_manual_assertion|ENST00000406921|protein_coding||c.3167-1G>A||||||,T|upstream_gene_variant|MODIFIER|ITSN2|ENSG00000198399|transcript|ENST00000416160|protein_coding||c.-54G>A|||||52|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ITSN2|ENSG00000198399|12|0.25) GT:AD:AF:DP 0/1:64,21:0.23:85 0/0:32,0:0:32 | |
| chr2 24993141 . G T . t_lod_fstar ClippingRankSum=0;DP=220;ECNT=1;FS=10.611;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.74;ReadPosRankSum=0.316;TLOD=4.40;ANN=T|3_prime_UTR_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000348332|protein_coding|21/21|c.*1881G>T|||||1881|,T|3_prime_UTR_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000406961|protein_coding|23/23|c.*1881G>T|||||1881|,T|3_prime_UTR_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000405141|protein_coding|25/25|c.*2064G>T|||||2149|,T|3_prime_UTR_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000288599|protein_coding|22/22|c.*2064G>T|||||2149|,T|3_prime_UTR_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000395856|protein_coding|21/21|c.*1881G>T|||||1881|,T|downstream_gene_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000407230|protein_coding||c.*2149G>T|||||1729|,T|downstream_gene_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000538539|protein_coding||c.*2149G>T|||||1955|,T|downstream_gene_variant|MODIFIER|NCOA1|ENSG00000084676|transcript|ENST00000493773|retained_intron||n.*1884G>T|||||1884| GT:AD:AF:DP 0/1:149,3:0.028:152 0/0:68,0:0:68 | |
| chr2 26022303 . ACTG A . PASS ClippingRankSum=0;DP=137;ECNT=1;FS=2.083;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.23;ReadPosRankSum=-0.598;TLOD=8.20;ANN=A|disruptive_inframe_deletion|MODERATE|ASXL2|ENSG00000143970|transcript|ENST00000435504|protein_coding|5/13|c.351_353delCAG|p.Ser118del|647/12878|351/4308|117/1435||,A|disruptive_inframe_deletion|MODERATE|ASXL2|ENSG00000143970|transcript|ENST00000336112|protein_coding|4/12|c.267_269delCAG|p.Ser90del|597/8889|267/4224|89/1407||,A|5_prime_UTR_variant|MODIFIER|ASXL2|ENSG00000143970|transcript|ENST00000272341|protein_coding|4/13|c.-430_-428delCAG|||||39795|,A|non_coding_transcript_exon_variant|MODIFIER|ASXL2|ENSG00000143970|transcript|ENST00000497092|processed_transcript|3/5|n.289_291delCAG|||||| GT:AD:AF:DP 0/1:84,4:0.045:88 0/0:48,0:0:48 | |
| chr2 26703835 . C T . PASS ClippingRankSum=0;DP=33;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.41;ReadPosRankSum=-0.08;TLOD=14.67;ANN=T|missense_variant|MODERATE|OTOF|ENSG00000115155|transcript|ENST00000272371|protein_coding|15/47|c.1622G>A|p.Gly541Asp|1749/7156|1622/5994|541/1997||,T|missense_variant|MODERATE|OTOF|ENSG00000115155|transcript|ENST00000403946|protein_coding|15/46|c.1622G>A|p.Gly541Asp|1729/6937|1622/5994|541/1997||,T|upstream_gene_variant|MODIFIER|OTOF|ENSG00000115155|transcript|ENST00000338581|protein_coding||c.-3245G>A|||||2925|,T|upstream_gene_variant|MODIFIER|OTOF|ENSG00000115155|transcript|ENST00000339598|protein_coding||c.-3245G>A|||||2925|,T|upstream_gene_variant|MODIFIER|OTOF|ENSG00000115155|transcript|ENST00000402415|protein_coding||c.-3074G>A|||||2925| GT:AD:AF:DP 0/1:12,10:0.5:22 0/0:11,0:0:11 | |
| chr2 27351849 . G T . t_lod_fstar ClippingRankSum=0;DP=149;ECNT=1;FS=0;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.53;ReadPosRankSum=0.17;TLOD=5.46;ANN=T|synonymous_variant|LOW|ABHD1|ENSG00000143994|transcript|ENST00000316470|protein_coding|3/9|c.312G>T|p.Leu104Leu|426/1400|312/1218|104/405||,T|synonymous_variant|LOW|ABHD1|ENSG00000143994|transcript|ENST00000448950|nonsense_mediated_decay|3/8|c.312G>T|p.Leu104Leu|438/1387|312/918|104/305||,T|synonymous_variant|LOW|ABHD1|ENSG00000143994|transcript|ENST00000420647|nonsense_mediated_decay|2/6|c.123G>T|p.Leu41Leu|264/1167|123/309|41/102||,T|synonymous_variant|LOW|ABHD1|ENSG00000143994|transcript|ENST00000416071|protein_coding|2/5|c.123G>T|p.Leu41Leu|260/668|123/531|41/176||WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ABHD1|ENSG00000143994|transcript|ENST00000496739|retained_intron||n.-1134G>T|||||1134|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000260643|protein_coding||c.*2433C>A|||||1775|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000468045|retained_intron||n.*1775C>A|||||1775|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000444452|nonsense_mediated_decay||c.*4656C>A|||||1784|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000406567|protein_coding||c.*2433C>A|||||1794|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000456259|protein_coding||c.*2386C>A|||||1810|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000430533|protein_coding||c.*2474C>A|||||2178|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000441451|nonsense_mediated_decay||c.*3082C>A|||||2459|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000474802|retained_intron||n.*3530C>A|||||3530|,T|downstream_gene_variant|MODIFIER|PREB|ENSG00000138073|transcript|ENST00000416802|processed_transcript||n.*4143C>A|||||4143|,T|non_coding_transcript_exon_variant|MODIFIER|ABHD1|ENSG00000143994|transcript|ENST00000489120|retained_intron|3/3|n.447G>T|||||| GT:AD:AF:DP 0/1:95,4:0.046:99 0/0:50,0:0:50 | |
| chr2 27606852 . CTCT C . t_lod_fstar ClippingRankSum=0;DP=223;ECNT=1;FS=0;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.62;ReadPosRankSum=-0.801;TLOD=4.90;ANN=C|disruptive_inframe_deletion|MODERATE|PPM1G|ENSG00000115241|transcript|ENST00000344034|protein_coding|6/10|c.930_932delAGA|p.Glu311del|1197/2311|930/1641|310/546||,C|disruptive_inframe_deletion|MODERATE|PPM1G|ENSG00000115241|transcript|ENST00000350803|protein_coding|7/11|c.930_932delAGA|p.Glu311del|1039/2146|930/1641|310/546||,C|upstream_gene_variant|MODIFIER|ZNF513|ENSG00000163795|transcript|ENST00000323703|protein_coding||c.-3462_-3460delAGA|||||3261|,C|upstream_gene_variant|MODIFIER|ZNF513|ENSG00000163795|transcript|ENST00000407879|protein_coding||c.-3871_-3869delAGA|||||3542|,C|upstream_gene_variant|MODIFIER|ZNF513|ENSG00000163795|transcript|ENST00000491924|processed_transcript||n.-4995_-4993delAGA|||||4993|,C|upstream_gene_variant|MODIFIER|ZNF513|ENSG00000163795|transcript|ENST00000436006|protein_coding||c.-3871_-3869delAGA|||||3196|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PPM1G|ENSG00000115241|transcript|ENST00000484925|retained_intron||n.*2608_*2610delAGA|||||2610|,C|non_coding_transcript_exon_variant|MODIFIER|PPM1G|ENSG00000115241|transcript|ENST00000472077|retained_intron|4/8|n.2637_2639delAGA|||||| GT:AD:AF:DP 0/1:129,3:0.024:132 0/0:64,0:0:64 | |
| chr2 32696246 . G T . t_lod_fstar ClippingRankSum=0;DP=40;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=-0.101;TLOD=4.08;ANN=T|upstream_gene_variant|MODIFIER|BIRC6|ENSG00000115760|transcript|ENST00000462504|retained_intron||n.-1814G>T|||||1814|,T|intron_variant|MODIFIER|BIRC6|ENSG00000115760|transcript|ENST00000421745|protein_coding|32/73|c.6592+54G>T|||||| GT:AD:AF:DP 0/1:23,2:0.118:25 0/0:15,0:0:15 | |
| chr2 38830019 . CCCT C . PASS ClippingRankSum=0;DP=433;ECNT=1;FS=6.086;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60.05;MQ0=0;MQRankSum=10.149;NLOD=18.97;ReadPosRankSum=-1.639;TLOD=6.79;ANN=C|5_prime_UTR_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000449105|protein_coding|1/13|c.-254_-252delAGG|||||252|,C|5_prime_UTR_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000409636|protein_coding|1/14|c.-13_-11delAGG|||||11|,C|5_prime_UTR_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000608859|protein_coding|1/13|c.-254_-252delAGG|||||252|,C|5_prime_UTR_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000358367|protein_coding|1/7|c.-254_-252delAGG|||||252|,C|5_prime_UTR_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000410076|protein_coding|1/7|c.-13_-11delAGG|||||11|,C|upstream_gene_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000378915|protein_coding||c.-254_-252delAGG|||||252|,C|upstream_gene_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000409328|protein_coding||c.-254_-252delAGG|||||21|,C|upstream_gene_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000425682|protein_coding||c.-2977_-2975delAGG|||||2852|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|AC011247.3|ENSG00000235586|transcript|ENST00000457097|antisense||n.*700_*702delCCT|||||700|,C|intron_variant|MODIFIER|HNRNPLL|ENSG00000143889|transcript|ENST00000498516|processed_transcript|1/2|n.420-280_420-278delAGG|||||| GT:AD:AF:DP 0/1:280,5:0.016:285 0/0:130,3:0.022:133 | |
| chr2 40403063 . G T . t_lod_fstar ClippingRankSum=0;DP=108;ECNT=1;FS=1.703;HCNT=26;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.08;ReadPosRankSum=-1.207;TLOD=5.22;ANN=T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000444629|antisense|1/2|n.54+70961G>T||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000332839|protein_coding|2/9|c.1916-642C>A||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000599740|antisense|1/1|n.74-75761G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000599268|antisense|2/2|n.563+70961G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000597385|antisense|3/4|n.277-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000601679|antisense|3/4|n.405-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000593878|antisense|5/7|n.525-34044G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000596532|antisense|6/7|n.550-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000597170|antisense|2/4|n.105-34044G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000599956|antisense|3/4|n.207-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000406785|protein_coding|3/7|c.1913-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000542756|protein_coding|3/9|c.1916-642C>A||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000598247|antisense|1/2|n.617-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000407929|nonsense_mediated_decay|3/7|c.*16-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000593848|antisense|1/5|n.220-32452G>T||||||,T|intron_variant|MODIFIER|SLC8A1-AS1|ENSG00000227028|transcript|ENST00000435515|antisense|1/3|n.126-47707G>T||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000403092|protein_coding|3/10|c.1916-642C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000405901|protein_coding|2/8|c.1916-642C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000402441|protein_coding|3/7|c.1913-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000405269|protein_coding|3/7|c.1913-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000406391|protein_coding|2/6|c.1913-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000408028|protein_coding|2/8|c.1913-1081C>A||||||,T|intron_variant|MODIFIER|SLC8A1|ENSG00000183023|transcript|ENST00000542024|protein_coding|3/6|c.1922+54C>A|||||| GT:AD:AF:DP 0/1:64,5:0.065:69 0/0:39,0:0:39 | |
| chr2 42511743 . G T . t_lod_fstar ClippingRankSum=0;DP=284;ECNT=1;FS=0;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.05;ReadPosRankSum=0.099;TLOD=4.70;ANN=T|upstream_gene_variant|MODIFIER|EML4|ENSG00000143924|transcript|ENST00000406175|retained_intron||n.-1320G>T|||||1320|,T|intron_variant|MODIFIER|EML4|ENSG00000143924|transcript|ENST00000401738|protein_coding|9/23|c.975-31G>T||||||,T|intron_variant|MODIFIER|EML4|ENSG00000143924|transcript|ENST00000318522|protein_coding|8/22|c.942-31G>T||||||,T|intron_variant|MODIFIER|EML4|ENSG00000143924|transcript|ENST00000402711|protein_coding|7/21|c.768-31G>T||||||,T|intron_variant|MODIFIER|EML4|ENSG00000143924|transcript|ENST00000480320|retained_intron|1/3|n.65-31G>T|||||| GT:AD:AF:DP 0/1:194,3:0.022:197 0/0:87,0:0:87 | |
| chr2 43726118 . G T . t_lod_fstar ClippingRankSum=0;DP=125;ECNT=1;FS=0;HCNT=52;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.72;ReadPosRankSum=-0.044;TLOD=5.37;ANN=T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000405006|protein_coding|24/37|c.3622-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000330266|protein_coding|15/19|c.2752-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000405975|protein_coding|24/37|c.3622-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000415080|protein_coding|24/37|c.2752-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000407351|protein_coding|11/22|c.1561-24C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000398653|nonsense_mediated_decay|24/35|c.*2720-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000408045|nonsense_mediated_decay|24/29|c.*2717-24C>A||||||,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000402796|nonsense_mediated_decay|13/17|c.*933-24C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|THADA|ENSG00000115970|transcript|ENST00000436947|processed_transcript|2/4|n.221-24C>A|||||| GT:AD:AF:DP 0/1:83,4:0.05:87 0/0:38,0:0:38 | |
| chr2 43989407 . G T . t_lod_fstar ClippingRankSum=0;DP=204;ECNT=1;FS=1.809;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=16.25;ReadPosRankSum=0.707;TLOD=4.51;ANN=T|intron_variant|MODIFIER|PLEKHH2|ENSG00000152527|transcript|ENST00000282406|protein_coding|27/29|c.4072-36G>T||||||,T|intron_variant|MODIFIER|PLEKHH2|ENSG00000152527|transcript|ENST00000405000|retained_intron|27/29|n.6081-36G>T||||||,T|intron_variant|MODIFIER|PLEKHH2|ENSG00000152527|transcript|ENST00000490038|nonsense_mediated_decay|3/5|c.*71-36G>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:131,5:0.03:136 0/0:68,0:0:68 | |
| chr2 44055065 . GCA G . t_lod_fstar ClippingRankSum=0;DP=130;ECNT=1;FS=0;HCNT=45;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=0.366;TLOD=4.04;ANN=G|intron_variant|MODIFIER|ABCG5|ENSG00000138075|transcript|ENST00000260645|protein_coding|5/12|c.634+55_634+56delTG||||||,G|intron_variant|MODIFIER|ABCG5|ENSG00000138075|transcript|ENST00000486512|nonsense_mediated_decay|4/8|c.*387+55_*387+56delTG||||||,G|intron_variant|MODIFIER|ABCG5|ENSG00000138075|transcript|ENST00000543989|protein_coding|4/8|c.-68+55_-68+56delTG||||||,G|intron_variant|MODIFIER|ABCG5|ENSG00000138075|transcript|ENST00000405322|protein_coding|4/9|c.391+55_391+56delTG||||||,G|intron_variant|MODIFIER|ABCG5|ENSG00000138075|transcript|ENST00000409962|nonsense_mediated_decay|4/8|c.391+55_391+56delTG|||||| GT:AD:AF:DP 0/1:87,2:0.033:89 0/0:35,0:0:35 | |
| chr2 44471326 . CAT C . PASS ClippingRankSum=0;DP=129;ECNT=1;FS=1.447;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.77;ReadPosRankSum=0.497;TLOD=9.40;ANN=C|upstream_gene_variant|MODIFIER|snoU13|ENSG00000239052|transcript|ENST00000459048|snoRNA||n.-4528_-4527delAT|||||4527|,C|intron_variant|MODIFIER|PPM1B|ENSG00000138032|transcript|ENST00000378540|processed_transcript|5/5|n.1547-26_1547-25delAT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|PPM1B|ENSG00000138032|transcript|ENST00000487286|processed_transcript|5/5|n.380-26_380-25delAT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:97,8:0.089:105 0/0:20,1:0.05:21 | |
| chr2 44571743 . C T . t_lod_fstar ClippingRankSum=0;DP=515;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=30.69;ReadPosRankSum=0.522;TLOD=5.49;ANN=T|downstream_gene_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000477410|processed_transcript||n.*1695G>A|||||1695|,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000260648|protein_coding|2/13|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000425263|nonsense_mediated_decay|2/14|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000426481|nonsense_mediated_decay|2/14|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000541738|protein_coding|2/13|c.76-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000409411|protein_coding|2/13|c.76-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000409957|protein_coding|2/13|c.76-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000409936|protein_coding|3/14|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000409272|protein_coding|3/14|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000410081|protein_coding|3/14|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000378520|protein_coding|2/12|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000378511|protein_coding|2/12|c.343-18G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000540817|processed_transcript|2/2|n.414-653G>A||||||,T|intron_variant|MODIFIER|PREPL|ENSG00000138078|transcript|ENST00000438314|protein_coding|4/5|c.343-18G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:364,8:0.02:372 0/0:143,0:0:143 | |
| chr2 46844373 . CCTG C . PASS ClippingRankSum=0;DP=50;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.00;ReadPosRankSum=-0.885;TLOD=9.70;ANN=C|5_prime_UTR_variant|MODIFIER|CRIPT|ENSG00000119878|transcript|ENST00000238892|protein_coding|1/5|c.-33_-31delCTG|||||31|INFO_REALIGN_3_PRIME,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000281382|protein_coding||c.-2073_-2071delCAG|||||116|,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000420164|nonsense_mediated_decay||c.-4963_-4961delCAG|||||4961|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000306465|protein_coding||c.-2073_-2071delCAG|||||184|,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000412717|nonsense_mediated_decay||c.-2073_-2071delCAG|||||180|,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000495933|processed_transcript||n.-207_-205delCAG|||||205|,C|upstream_gene_variant|MODIFIER|PIGF|ENSG00000151665|transcript|ENST00000474980|protein_coding||c.-2073_-2071delCAG|||||198|WARNING_TRANSCRIPT_NO_STOP_CODON,C|intron_variant|MODIFIER|CRIPT|ENSG00000119878|transcript|ENST00000486447|processed_transcript|1/4|n.608+227_608+229delCTG||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:27,3:0.136:30 0/0:14,0:0:14 | |
| chr2 50148613 . G T . t_lod_fstar ClippingRankSum=0;DP=158;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.53;ReadPosRankSum=0.881;TLOD=4.74;ANN=T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000404971|protein_coding|24/24|c.*469C>A|||||469|,T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000342183|protein_coding|6/6|c.*469C>A|||||469|,T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000412315|protein_coding|3/3|c.*469C>A|||||469|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000378262|protein_coding|3/3|c.*469C>A|||||469|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000401710|protein_coding|9/9|c.*469C>A|||||469|,T|3_prime_UTR_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000406316|protein_coding|22/22|c.*469C>A|||||469|,T|downstream_gene_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000405472|protein_coding||c.*469C>A|||||294|,T|downstream_gene_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000401669|protein_coding||c.*469C>A|||||294|,T|downstream_gene_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000402717|protein_coding||c.*469C>A|||||469|,T|downstream_gene_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000406859|protein_coding||c.*469C>A|||||469|,T|non_coding_transcript_exon_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000484192|processed_transcript|3/3|n.1055C>A|||||| GT:AD:AF:DP 0/1:108,3:0.039:111 0/0:47,0:0:47 | |
| chr2 50755683 . GCT G . t_lod_fstar ClippingRankSum=0;DP=86;ECNT=1;FS=2.062;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.52;ReadPosRankSum=1.693;TLOD=5.86;ANN=G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000404971|protein_coding|13/23|c.2494+78_2494+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000406316|protein_coding|12/21|c.2374+78_2374+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000405472|protein_coding|11/21|c.2350+78_2350+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000401669|protein_coding|12/22|c.2374+78_2374+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000402717|protein_coding|12/22|c.2350+78_2350+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000406859|protein_coding|13/22|c.2374+78_2374+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000331040|processed_transcript|6/13|n.1554+2680_1554+2681delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000474354|retained_intron|1/2|n.311+78_311+79delAG||||||,G|intron_variant|MODIFIER|NRXN1|ENSG00000179915|transcript|ENST00000495871|processed_transcript|2/2|n.470+24040_470+24041delAG|||||| GT:AD:AF:DP 0/1:51,5:0.086:56 0/0:29,0:0:29 | |
| chr2 54888534 . A T . PASS ClippingRankSum=0;DP=87;ECNT=1;FS=2.218;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.52;ReadPosRankSum=-0.566;TLOD=35.62;ANN=T|3_prime_UTR_variant|MODIFIER|SPTBN1|ENSG00000115306|transcript|ENST00000333896|protein_coding|31/31|c.*1311A>T|||||1311|,T|upstream_gene_variant|MODIFIER|SPTBN1|ENSG00000115306|transcript|ENST00000467371|retained_intron||n.-1504A>T|||||1504|,T|downstream_gene_variant|MODIFIER|SPTBN1|ENSG00000115306|transcript|ENST00000496323|retained_intron||n.*1107A>T|||||1107|,T|intron_variant|MODIFIER|SPTBN1|ENSG00000115306|transcript|ENST00000356805|protein_coding|32/35|c.6420+1398A>T||||||,T|intron_variant|MODIFIER|AC093110.3|ENSG00000238018|transcript|ENST00000456363|antisense|1/1|n.238-22T>A|||||| GT:AD:AF:DP 0/1:34,19:0.35:53 0/0:34,0:0:34 | |
| chr2 55561560 . G T . t_lod_fstar ClippingRankSum=0;DP=154;ECNT=1;FS=2.053;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=0.535;TLOD=4.38;ANN=T|missense_variant|MODERATE|CCDC88A|ENSG00000115355|transcript|ENST00000436346|protein_coding|15/33|c.2397C>A|p.Asn799Lys|3239/9811|2397/5616|799/1871||,T|missense_variant|MODERATE|CCDC88A|ENSG00000115355|transcript|ENST00000336838|protein_coding|15/33|c.2397C>A|p.Asn799Lys|2931/9505|2397/5613|799/1870||,T|missense_variant|MODERATE|CCDC88A|ENSG00000115355|transcript|ENST00000263630|protein_coding|15/32|c.2397C>A|p.Asn799Lys|3174/9667|2397/5532|799/1843||,T|missense_variant|MODERATE|CCDC88A|ENSG00000115355|transcript|ENST00000413716|protein_coding|15/34|c.2397C>A|p.Asn799Lys|2594/6378|2397/5391|799/1796||,T|upstream_gene_variant|MODIFIER|CCDC88A|ENSG00000115355|transcript|ENST00000426576|protein_coding||c.-79C>A|||||79|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|CCDC88A|ENSG00000115355|transcript|ENST00000468534|retained_intron||n.-74C>A|||||74|,T|intron_variant|MODIFIER|AC012358.8|ENSG00000240401|transcript|ENST00000599475|antisense|1/1|n.171-5079G>T||||||,T|intron_variant|MODIFIER|AC012358.8|ENSG00000240401|transcript|ENST00000608103|antisense|3/3|n.506+2163G>T||||||,T|intron_variant|MODIFIER|AC012358.8|ENSG00000240401|transcript|ENST00000599352|antisense|2/2|n.382+4711G>T||||||,T|intron_variant|MODIFIER|AC012358.8|ENSG00000240401|transcript|ENST00000600219|antisense|2/2|n.188+4905G>T||||||,T|intron_variant|MODIFIER|AC012358.8|ENSG00000240401|transcript|ENST00000594078|antisense|1/1|n.91-10933G>T|||||| GT:AD:AF:DP 0/1:121,4:0.032:125 0/0:29,0:0:29 | |
| chr2 61009952 . A T . t_lod_fstar ClippingRankSum=0;DP=81;ECNT=1;FS=1.667;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.07;ReadPosRankSum=0.53;TLOD=4.83;ANN=T|sequence_feature|LOW|PAPOLG|ENSG00000115421|beta-strand:combinatorial_evidence_used_in_manual_assertion|ENST00000238714|protein_coding||c.1112+47A>T||||||,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000238714|protein_coding|12/21|c.1112+47A>T||||||,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000496283|retained_intron|11/18|n.1080+47A>T||||||,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000414060|nonsense_mediated_decay|11/20|c.*202+47A>T||||||,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000453839|nonsense_mediated_decay|10/19|c.*475+47A>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000483370|processed_transcript|4/4|n.501+47A>T||||||,T|intron_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000412217|protein_coding|2/10|c.116+47A>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:50,6:0.071:56 0/0:18,0:0:18 | |
| chr2 61020769 . G T . t_lod_fstar ClippingRankSum=0;DP=439;ECNT=1;FS=0;HCNT=31;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=27.94;ReadPosRankSum=-0.513;TLOD=4.27;ANN=T|missense_variant|MODERATE|PAPOLG|ENSG00000115421|transcript|ENST00000238714|protein_coding|18/22|c.1687G>T|p.Ala563Ser|1936/4263|1687/2211|563/736||,T|missense_variant|MODERATE|PAPOLG|ENSG00000115421|transcript|ENST00000412217|protein_coding|8/11|c.691G>T|p.Ala231Ser|691/6074|691/1149|231/382||WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000414060|nonsense_mediated_decay|17/21|c.*777G>T|||||11746|,T|3_prime_UTR_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000453839|nonsense_mediated_decay|15/20|c.*940G>T|||||18568|WARNING_TRANSCRIPT_NO_START_CODON,T|non_coding_transcript_exon_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000496283|retained_intron|17/19|n.1655G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|PAPOLG|ENSG00000115421|transcript|ENST00000470208|retained_intron|3/4|n.571G>T|||||| GT:AD:AF:DP 0/1:290,6:0.016:296 0/0:142,0:0:142 | |
| chr2 64778671 . GGAT G . t_lod_fstar ClippingRankSum=0;DP=127;ECNT=1;FS=2.284;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.82;ReadPosRankSum=-0.549;TLOD=5.31;ANN=G|disruptive_inframe_deletion|MODERATE|AFTPH|ENSG00000119844|transcript|ENST00000422803|protein_coding|2/10|c.78_80delTGA|p.Asp26del|392/4090|78/2814|26/937||INFO_REALIGN_3_PRIME,G|disruptive_inframe_deletion|MODERATE|AFTPH|ENSG00000119844|transcript|ENST00000238855|protein_coding|2/10|c.78_80delTGA|p.Asp26del|392/4087|78/2811|26/936||INFO_REALIGN_3_PRIME,G|disruptive_inframe_deletion|MODERATE|AFTPH|ENSG00000119844|transcript|ENST00000238856|protein_coding|2/9|c.78_80delTGA|p.Asp26del|392/4014|78/2730|26/909||INFO_REALIGN_3_PRIME,G|disruptive_inframe_deletion|MODERATE|AFTPH|ENSG00000119844|transcript|ENST00000409933|protein_coding|1/9|c.78_80delTGA|p.Asp26del|78/2811|78/2811|26/936||INFO_REALIGN_3_PRIME,G|upstream_gene_variant|MODIFIER|AFTPH|ENSG00000119844|transcript|ENST00000409183|protein_coding||c.-1044_-1042delGAT|||||974|,G|upstream_gene_variant|MODIFIER|AFTPH|ENSG00000119844|transcript|ENST00000487769|processed_transcript||n.-1338_-1336delGAT|||||1338|,G|non_coding_transcript_exon_variant|MODIFIER|AFTPH|ENSG00000119844|transcript|ENST00000498706|retained_intron|2/9|n.196_198delTGA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:75,3:0.038:78 0/0:36,0:0:36 | |
| chr2 64862658 . GAT G . t_lod_fstar ClippingRankSum=0;DP=425;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.14;ReadPosRankSum=0.508;TLOD=4.52;ANN=G|3_prime_UTR_variant|MODIFIER|SERTAD2|ENSG00000179833|transcript|ENST00000313349|protein_coding|2/2|c.*401_*402delAT|||||401|,G|downstream_gene_variant|MODIFIER|SERTAD2|ENSG00000179833|transcript|ENST00000476805|processed_transcript||n.*1007_*1008delAT|||||1008| GT:AD:AF:DP 0/1:232,4:0.02:236 0/0:125,3:0.023:128 | |
| chr2 68269598 . C T . PASS ClippingRankSum=0;DP=576;ECNT=1;FS=10.902;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=57.35;MQ0=34;MQRankSum=-6.359;NLOD=29.45;ReadPosRankSum=1.874;TLOD=11.51;ANN=T|3_prime_UTR_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000407324|protein_coding|6/6|c.*423G>A|||||423|,T|3_prime_UTR_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000355848|protein_coding|5/5|c.*423G>A|||||423|,T|downstream_gene_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000410067|protein_coding||c.*423G>A|||||190|,T|downstream_gene_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000409302|protein_coding||c.*423G>A|||||211|,T|downstream_gene_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000479484|retained_intron||n.*248G>A|||||248|,T|downstream_gene_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000485709|retained_intron||n.*366G>A|||||366|,T|downstream_gene_variant|MODIFIER|C1D|ENSG00000197223|transcript|ENST00000470189|processed_transcript||n.*4811G>A|||||4811| GT:AD:AF:DP 0/1:343,8:0.033:351 0/0:178,10:0.044:188 | |
| chr2 68406101 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=221;ECNT=6;FS=337.526;HCNT=63;MAX_ED=10;MIN_ED=1;MQ=57.98;MQ0=5;MQRankSum=-4.339;NLOD=4.82;ReadPosRankSum=5.906;TLOD=101.47;ANN=A|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1994A>T|||||1994|,A|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-864T>A|||||864|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4167T>A|||||2731|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1994A>T|||||1835|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4005T>A|||||4005|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1994A>T|||||1978|,A|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7499A>T|||||| GT:AD:AF:DP 0/1:104,45:0.301:149 0/0:40,2:0.053:42 | |
| chr2 68406102 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=221;ECNT=6;FS=167.79;HCNT=35;MAX_ED=10;MIN_ED=1;MQ=57.98;MQ0=5;MQRankSum=-5.566;NLOD=10.84;ReadPosRankSum=5.027;TLOD=26.71;ANN=A|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1993G>T|||||1993|,A|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-863C>A|||||863|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4168C>A|||||2732|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1993G>T|||||1834|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4006C>A|||||4006|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1993G>T|||||1977|,A|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7498G>T|||||| GT:AD:AF:DP 0/1:119,25:0.177:144 0/0:41,1:0.026:42 | |
| chr2 68406105 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=213;ECNT=6;FS=355.383;HCNT=62;MAX_ED=10;MIN_ED=1;MQ=57.9;MQ0=5;MQRankSum=-4.175;NLOD=2.30;ReadPosRankSum=5.981;TLOD=113.25;ANN=A|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1990A>T|||||1990|,A|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-860T>A|||||860|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4171T>A|||||2735|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1990A>T|||||1831|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4009T>A|||||4009|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1990A>T|||||1974|,A|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7495A>T|||||| GT:AD:AF:DP 0/1:99,45:0.313:144 0/0:37,3:0.083:40 | |
| chr2 68406106 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=211;ECNT=6;FS=156.881;HCNT=40;MAX_ED=10;MIN_ED=1;MQ=57.88;MQ0=5;MQRankSum=-2.636;NLOD=6.38;ReadPosRankSum=5.555;TLOD=30.07;ANN=A|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1989A>T|||||1989|,A|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-859T>A|||||859|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4172T>A|||||2736|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1989A>T|||||1830|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4010T>A|||||4010|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1989A>T|||||1973|,A|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7494A>T|||||| GT:AD:AF:DP 0/1:116,23:0.173:139 0/0:38,2:0.054:40 | |
| chr2 68406108 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=209;ECNT=6;FS=176.156;HCNT=41;MAX_ED=10;MIN_ED=1;MQ=57.86;MQ0=5;MQRankSum=-2.532;NLOD=6.08;ReadPosRankSum=5.489;TLOD=30.33;ANN=A|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1987G>T|||||1987|,A|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-857C>A|||||857|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4174C>A|||||2738|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1987G>T|||||1828|,A|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4012C>A|||||4012|,A|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1987G>T|||||1971|,A|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7492G>T|||||| GT:AD:AF:DP 0/1:107,23:0.176:130 0/0:38,2:0.056:40 | |
| chr2 68406111 . A C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=207;ECNT=6;FS=92.279;HCNT=19;MAX_ED=10;MIN_ED=1;MQ=57.9;MQ0=5;MQRankSum=-3.537;NLOD=10.83;ReadPosRankSum=2.915;TLOD=13.48;ANN=C|3_prime_UTR_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000234310|protein_coding|6/6|c.*1984T>G|||||1984|,C|upstream_gene_variant|MODIFIER|RP11-474G23.2|ENSG00000273275|transcript|ENST00000609955|antisense||n.-854A>C|||||854|,C|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000263657|protein_coding||c.*4177A>C|||||2741|,C|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409752|protein_coding||c.*1984T>G|||||1825|,C|downstream_gene_variant|MODIFIER|PNO1|ENSG00000115946|transcript|ENST00000488728|retained_intron||n.*4015A>C|||||4015|,C|downstream_gene_variant|MODIFIER|PPP3R1|ENSG00000221823|transcript|ENST00000409377|protein_coding||c.*1984T>G|||||1968|,C|intron_variant|MODIFIER|RP11-474G23.1|ENSG00000273398|transcript|ENST00000406334|nonsense_mediated_decay|6/14|c.435+7489T>G|||||| GT:AD:AF:DP 0/1:116,15:0.107:131 0/0:40,0:0:40 | |
| chr2 68756088 . T C . t_lod_fstar ClippingRankSum=0;DP=359;ECNT=1;FS=19.28;HCNT=26;MAX_ED=.;MIN_ED=.;MQ=54.37;MQ0=9;MQRankSum=-3.492;NLOD=19.28;ReadPosRankSum=-4.187;TLOD=5.14;ANN=C|upstream_gene_variant|MODIFIER|APLF|ENSG00000169621|transcript|ENST00000471727|processed_transcript||n.-682T>C|||||682|,C|intron_variant|MODIFIER|APLF|ENSG00000169621|transcript|ENST00000303795|protein_coding|6/9|c.804+2714T>C||||||,C|intron_variant|MODIFIER|APLF|ENSG00000169621|transcript|ENST00000529851|nonsense_mediated_decay|5/8|c.*178+2714T>C||||||,C|intron_variant|MODIFIER|APLF|ENSG00000169621|transcript|ENST00000445692|nonsense_mediated_decay|6/10|c.804+2714T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC130709.1|ENSG00000214525|transcript|ENST00000484779|processed_pseudogene|1/1|n.497A>G|||||| GT:AD:AF:DP 0/1:225,6:0.034:231 0/0:112,3:0.034:115 | |
| chr2 69597136 . G T . t_lod_fstar ClippingRankSum=0;DP=189;ECNT=1;FS=5.558;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.84;ReadPosRankSum=0.247;TLOD=5.07;ANN=T|missense_variant|MODERATE|GFPT1|ENSG00000198380|transcript|ENST00000357308|protein_coding|3/20|c.220C>A|p.His74Asn|399/8695|220/2100|74/699||,T|missense_variant|MODERATE|GFPT1|ENSG00000198380|transcript|ENST00000361060|protein_coding|3/19|c.220C>A|p.His74Asn|397/8632|220/2046|74/681||,T|non_coding_transcript_exon_variant|MODIFIER|GFPT1|ENSG00000198380|transcript|ENST00000494201|processed_transcript|4/5|n.562C>A|||||| GT:AD:AF:DP 0/1:116,3:0.034:119 0/0:70,0:0:70 | |
| chr2 71627623 . C T . t_lod_fstar ClippingRankSum=0;DP=144;ECNT=1;FS=2.028;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.83;ReadPosRankSum=0.128;TLOD=4.88;ANN=T|missense_variant|MODERATE|ZNF638|ENSG00000075292|transcript|ENST00000264447|protein_coding|15/28|c.2672C>T|p.Ala891Val|2986/6505|2672/5937|891/1978||,T|missense_variant|MODERATE|ZNF638|ENSG00000075292|transcript|ENST00000355812|protein_coding|15/27|c.2672C>T|p.Ala891Val|2991/5281|2672/3420|891/1139||,T|missense_variant|MODERATE|ZNF638|ENSG00000075292|transcript|ENST00000409544|protein_coding|15/28|c.2672C>T|p.Ala891Val|3302/6821|2672/5937|891/1978||,T|upstream_gene_variant|MODIFIER|ZNF638|ENSG00000075292|transcript|ENST00000494241|retained_intron||n.-3357C>T|||||3357|,T|downstream_gene_variant|MODIFIER|ZNF638|ENSG00000075292|transcript|ENST00000410075|processed_transcript||n.*4827C>T|||||4827|,T|downstream_gene_variant|MODIFIER|ZNF638|ENSG00000075292|transcript|ENST00000491843|retained_intron||n.*1736C>T|||||1736|,T|non_coding_transcript_exon_variant|MODIFIER|ZNF638|ENSG00000075292|transcript|ENST00000487638|retained_intron|5/18|n.717C>T|||||| GT:AD:AF:DP 0/1:87,4:0.047:91 0/0:53,0:0:53 | |
| chr2 74041155 . G T . t_lod_fstar ClippingRankSum=0;DP=162;ECNT=1;FS=2.028;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.98;ReadPosRankSum=-0.672;TLOD=4.51;ANN=T|missense_variant|MODERATE|C2orf78|ENSG00000187833|transcript|ENST00000409561|protein_coding|2/3|c.649G>T|p.Gly217Cys|770/3045|649/2769|217/922|| GT:AD:AF:DP 0/1:114,4:0.038:118 0/0:43,0:0:43 | |
| chr2 74782262 . ACT A . t_lod_fstar ClippingRankSum=0;DP=36;ECNT=1;FS=2.153;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.01;ReadPosRankSum=0.736;TLOD=4.69;ANN=A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000233668|protein_coding|1/4|c.61-7_61-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000409429|protein_coding|1/4|c.-357-7_-357-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000485132|processed_transcript|3/3|n.328-7_328-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000488613|processed_transcript|2/2|n.482-9_482-8delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000340004|protein_coding|1/3|c.61-7_61-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000489958|processed_transcript|1/3|n.82-9_82-8delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000482206|retained_intron|1/1|n.123-7_123-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000474924|retained_intron|1/1|n.78-7_78-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000480318|processed_transcript|1/4|n.78-9_78-8delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000496966|processed_transcript|1/3|n.74-7_74-6delTC||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|DOK1|ENSG00000115325|transcript|ENST00000475191|retained_intron|1/3|n.111-9_111-8delTC||||||INFO_REALIGN_3_PRIME,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000264094|protein_coding||c.-2503_-2502delAG|||||1201|,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000409249|protein_coding||c.-2503_-2502delAG|||||2489|,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000393937|protein_coding||c.-2503_-2502delAG|||||1178|,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000409549|protein_coding||c.-2503_-2502delAG|||||2052|,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000409986|protein_coding||c.-2503_-2502delAG|||||1175|,A|upstream_gene_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000484369|processed_transcript||n.-2490_-2489delAG|||||2489|,A|upstream_gene_variant|MODIFIER|DOK1|ENSG00000115325|transcript|ENST00000429631|nonsense_mediated_decay||c.-72_-71delCT|||||70|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000290536|protein_coding||c.*3579_*3580delAG|||||2747|,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000464686|processed_transcript||n.*2755_*2756delAG|||||2756|,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000409585|protein_coding||c.*3579_*3580delAG|||||2756|,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000536235|protein_coding||c.*3579_*3580delAG|||||3202|,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000485997|processed_transcript||n.*3513_*3514delAG|||||3514|,A|downstream_gene_variant|MODIFIER|M1AP|ENSG00000159374|transcript|ENST00000358434|protein_coding||c.*3579_*3580delAG|||||3580|,A|intron_variant|MODIFIER|LOXL3|ENSG00000115318|transcript|ENST00000413469|protein_coding|1/4|c.-13+475_-13+476delAG||||||WARNING_TRANSCRIPT_INCOMPLETE,A|non_coding_transcript_exon_variant|MODIFIER|DOK1|ENSG00000115325|transcript|ENST00000464613|retained_intron|1/4|n.16_17delTC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:19,4:0.125:23 0/0:13,0:0:13 | |
| chr2 85133698 . AC A . t_lod_fstar ClippingRankSum=0;DP=265;ECNT=1;FS=2.846;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=59.89;MQ0=0;MQRankSum=0;NLOD=6.34;ReadPosRankSum=-0.007;TLOD=4.12;ANN=A|TF_binding_site_variant|LOW|||SP1|MA0079.1|||n.85133699delG||||||,A|3_prime_UTR_variant|MODIFIER|TMSB10|ENSG00000034510|transcript|ENST00000233143|protein_coding|3/3|c.*160delC|||||160|INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|TRABD2A|ENSG00000186854|transcript|ENST00000474298|processed_transcript|1/1|n.346+88delG||||||,A|intron_variant|MODIFIER|TRABD2A|ENSG00000186854|transcript|ENST00000489999|processed_transcript|1/1|n.346+88delG|||||| GT:AD:AF:DP 0/1:154,17:0.079:171 0/0:79,10:0.117:89 | |
| chr2 85893741 . G A . germline_risk ClippingRankSum=0;DP=16;ECNT=1;FS=1.987;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.903;ReadPosRankSum=-0.383;TLOD=11.73;ANN=A|missense_variant&splice_region_variant|MODERATE|SFTPB|ENSG00000168878|transcript|ENST00000393822|protein_coding|5/12|c.428C>T|p.Thr143Ile|528/3664|428/1182|143/393||,A|missense_variant&splice_region_variant|MODERATE|SFTPB|ENSG00000168878|transcript|ENST00000519937|protein_coding|4/11|c.392C>T|p.Thr131Ile|412/3554|392/1146|131/381||,A|missense_variant&splice_region_variant|MODERATE|SFTPB|ENSG00000168878|transcript|ENST00000342375|protein_coding|5/12|c.392C>T|p.Thr131Ile|528/3664|392/1146|131/381||,A|missense_variant&splice_region_variant|MODERATE|SFTPB|ENSG00000168878|transcript|ENST00000428225|protein_coding|4/11|c.380C>T|p.Thr127Ile|381/1743|380/1122|127/373||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant&splice_region_variant|MODERATE|SFTPB|ENSG00000168878|transcript|ENST00000409383|protein_coding|5/12|c.428C>T|p.Thr143Ile|528/1867|428/1182|143/393||,A|upstream_gene_variant|MODIFIER|SFTPB|ENSG00000168878|transcript|ENST00000494165|protein_coding||c.-3141C>T|||||3140|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|SFTPB|ENSG00000168878|transcript|ENST00000491167|retained_intron||n.-3071C>T|||||3071|,A|non_coding_transcript_exon_variant|MODIFIER|SFTPB|ENSG00000168878|transcript|ENST00000473692|retained_intron|4/4|n.398C>T|||||| GT:AD:AF:DP 0/1:5,6:0.571:11 0/0:5,0:0:5 | |
| chr2 86385682 . TC T . germline_risk ClippingRankSum=0;DP=156;ECNT=1;FS=4.019;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.522;ReadPosRankSum=-0.916;TLOD=15.17;ANN=T|sequence_feature|MODERATE|IMMT|ENSG00000132305|modified-residue:phosphoserine|ENST00000410111|protein_coding||c.1162+32delG||||||,T|sequence_feature|MODERATE|IMMT|ENSG00000132305|modified-residue:phosphoserine|ENST00000449247|protein_coding||c.1129+32delG||||||,T|sequence_feature|MODERATE|IMMT|ENSG00000132305|modified-residue:phosphoserine|ENST00000442664|protein_coding||c.1159+32delG||||||,T|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000200241|transcript|ENST00000363371|misc_RNA||n.*1396delG|||||1396|,T|downstream_gene_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000409258|nonsense_mediated_decay||c.*12799delG|||||687|,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000410111|protein_coding|10/14|c.1162+32delG||||||,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000254636|protein_coding|10/14|c.865+32delG||||||,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000449247|protein_coding|10/14|c.1129+32delG||||||,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000419070|protein_coding|6/10|c.724+32delG||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000442664|protein_coding|10/14|c.1159+32delG||||||,T|intron_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000409051|protein_coding|9/13|c.1021+32delG||||||,T|non_coding_transcript_exon_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000474969|retained_intron|10/10|n.1247delG||||||,T|non_coding_transcript_exon_variant|MODIFIER|IMMT|ENSG00000132305|transcript|ENST00000490238|processed_transcript|5/5|n.616delG|||||| GT:AD:AF:DP 0/1:35,56:0.652:91 0/0:35,19:0.359:54 | |
| chr2 87364797 . A T . PASS ClippingRankSum=0;DP=498;ECNT=1;FS=22.39;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=53.27;MQ0=30;MQRankSum=-2.906;NLOD=3.03;ReadPosRankSum=0.751;TLOD=24.76;ANN=T|intron_variant|MODIFIER|AC083899.3|ENSG00000204745|transcript|ENST00000454465|unprocessed_pseudogene|5/30|n.667+29A>T|||||| GT:AD:AF:DP 0/1:308,15:0.073:323 0/0:125,16:0.147:141 | |
| chr2 87365406 . T A . PASS ClippingRankSum=0;DP=341;ECNT=1;FS=2.948;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=50.6;MQ0=12;MQRankSum=0.928;NLOD=10.70;ReadPosRankSum=-0.387;TLOD=13.46;ANN=A|non_coding_transcript_exon_variant|MODIFIER|AC083899.3|ENSG00000204745|transcript|ENST00000454465|unprocessed_pseudogene|6/31|n.695T>A|||||| GT:AD:AF:DP 0/1:157,7:0.064:164 0/0:145,14:0.123:159 | |
| chr2 87607873 . G A . PASS ClippingRankSum=0;DP=2213;ECNT=1;FS=22.046;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=42.25;MQ0=299;MQRankSum=-3.963;NLOD=18.92;ReadPosRankSum=-2.379;TLOD=61.16;ANN=A|non_coding_transcript_exon_variant|MODIFIER|AC068279.3|ENSG00000224881|transcript|ENST00000444323|processed_pseudogene|1/1|n.18C>T|||||| GT:AD:AF:DP 0/1:1110,54:0.063:1164 0/0:639,45:0.085:684 | |
| chr2 88035183 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=248;ECNT=2;FS=54.259;HCNT=7;MAX_ED=60;MIN_ED=60;MQ=47.41;MQ0=29;MQRankSum=-3.55;NLOD=6.04;ReadPosRankSum=-3.105;TLOD=41.77;ANN=G|intron_variant|MODIFIER|AC093616.4|ENSG00000234231|transcript|ENST00000427434|unprocessed_pseudogene|12/14|n.1786-10C>G||||||,G|intron_variant|MODIFIER|AC093616.4|ENSG00000234231|transcript|ENST00000540487|unprocessed_pseudogene|3/6|n.629-10C>G|||||| GT:AD:AF:DP 0/1:83,22:0.247:105 0/0:86,17:0.176:103 | |
| chr2 88035243 . T G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=362;ECNT=2;FS=2.665;HCNT=14;MAX_ED=60;MIN_ED=60;MQ=42.58;MQ0=123;MQRankSum=2.209;NLOD=5.65;ReadPosRankSum=-2.488;TLOD=6.30;ANN=G|non_coding_transcript_exon_variant|MODIFIER|AC093616.4|ENSG00000234231|transcript|ENST00000427434|unprocessed_pseudogene|13/15|n.1836T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|AC093616.4|ENSG00000234231|transcript|ENST00000540487|unprocessed_pseudogene|4/7|n.679T>G|||||| GT:AD:AF:DP 0/1:78,4:0.073:82 0/0:127,23:0.167:150 | |
| chr2 88125215 . G C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=236;ECNT=2;FS=25.242;HCNT=2;MAX_ED=19;MIN_ED=19;MQ=50.56;MQ0=9;MQRankSum=-2.508;NLOD=1.61;ReadPosRankSum=-1.317;TLOD=9.12;ANN=C|missense_variant|MODERATE|RGPD2|ENSG00000185304|transcript|ENST00000398146|protein_coding|1/23|c.34C>G|p.Leu12Val|257/6931|34/5271|12/1756||,C|5_prime_UTR_variant|MODIFIER|RGPD2|ENSG00000185304|transcript|ENST00000327544|protein_coding|1/23|c.-2196C>G|||||33385|,C|downstream_gene_variant|MODIFIER|MTATP8P2|ENSG00000229604|transcript|ENST00000435212|processed_pseudogene||n.*553G>C|||||553|,C|intron_variant|MODIFIER|RGPD2|ENSG00000185304|transcript|ENST00000420840|protein_coding|1/22|c.49-7073C>G|||||| GT:AD:AF:DP 0/1:152,8:0.066:160 0/0:59,3:0.075:62 | |
| chr2 88125234 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=232;ECNT=2;FS=30.047;HCNT=4;MAX_ED=19;MIN_ED=19;MQ=49.67;MQ0=9;MQRankSum=-1.252;NLOD=1.85;ReadPosRankSum=-0.435;TLOD=34.13;ANN=C|synonymous_variant|LOW|RGPD2|ENSG00000185304|transcript|ENST00000398146|protein_coding|1/23|c.15A>G|p.Lys5Lys|238/6931|15/5271|5/1756||,C|5_prime_UTR_variant|MODIFIER|RGPD2|ENSG00000185304|transcript|ENST00000327544|protein_coding|1/23|c.-2215A>G|||||33404|,C|downstream_gene_variant|MODIFIER|MTATP8P2|ENSG00000229604|transcript|ENST00000435212|processed_pseudogene||n.*572T>C|||||572|,C|intron_variant|MODIFIER|RGPD2|ENSG00000185304|transcript|ENST00000420840|protein_coding|1/22|c.49-7092A>G|||||| GT:AD:AF:DP 0/1:141,15:0.131:156 0/0:48,13:0.205:61 | |
| chr2 88874268 . CCT C . t_lod_fstar ClippingRankSum=0;DP=92;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=1.201;TLOD=4.40;ANN=C|frameshift_variant|HIGH|EIF2AK3|ENSG00000172071|transcript|ENST00000303236|protein_coding|13/17|c.2731_2732delAG|p.Arg911fs|3034/4646|2731/3351|911/1116||,C|frameshift_variant|HIGH|EIF2AK3|ENSG00000172071|transcript|ENST00000419748|protein_coding|13/17|c.2278_2279delAG|p.Arg760fs|2608/4222|2278/2898|760/965||,C|frameshift_variant|HIGH|EIF2AK3|ENSG00000172071|transcript|ENST00000415570|protein_coding|12/16|c.2368_2369delAG|p.Arg790fs|2401/2902|2368/2870|790/955||WARNING_TRANSCRIPT_INCOMPLETE,C|structural_interaction_variant|HIGH|EIF2AK3|ENSG00000172071|interaction|4X7J:A_911-A_1050:ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|structural_interaction_variant|HIGH|EIF2AK3|ENSG00000172071|interaction|4X7K:A_911-A_1050:ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|structural_interaction_variant|HIGH|EIF2AK3|ENSG00000172071|interaction|4X7L:A_911-A_1050:ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|structural_interaction_variant|HIGH|EIF2AK3|ENSG00000172071|interaction|4X7N:A_911-A_1050:ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|structural_interaction_variant|HIGH|EIF2AK3|ENSG00000172071|interaction|4X7O:A_911-A_1050:ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|sequence_feature|LOW|EIF2AK3|ENSG00000172071|helix:combinatorial_evidence_used_in_manual_assertion|ENST00000303236|protein_coding|13/17|c.2731_2732delAG||||||,C|downstream_gene_variant|MODIFIER|EIF2AK3|ENSG00000172071|transcript|ENST00000478003|retained_intron||n.*631_*632delAG|||||632|,C|non_coding_transcript_exon_variant|MODIFIER|AC104134.2|ENSG00000225420|transcript|ENST00000413234|antisense|3/3|n.897_898delTC||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|EIF2AK3|ENSG00000172071|transcript|ENST00000470706|processed_transcript|2/3|n.374_375delAG||||||;LOF=(EIF2AK3|ENSG00000172071|6|0.50) GT:AD:AF:DP 0/1:47,3:0.063:50 0/0:34,0:0:34 | |
| chr2 89066856 . A C . clustered_events;t_lod_fstar ClippingRankSum=0;DP=248;ECNT=2;FS=16.6;HCNT=14;MAX_ED=4;MIN_ED=4;MQ=59.07;MQ0=1;MQRankSum=-9.413;NLOD=27.69;ReadPosRankSum=-1.416;TLOD=5.02;ANN=C|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|1/14|n.329+1143A>C||||||,C|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000421951|processed_transcript|1/3|n.390+1143A>C||||||,C|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000427055|processed_transcript|1/1|n.316+1143A>C||||||,C|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|1/16|n.295+1143A>C||||||,C|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000443770|processed_transcript|1/2|n.254+1143A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC096579.1|ENSG00000221686|transcript|ENST00000408759|miRNA|1/1|n.22A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:129,4:0.028:133:0|1:89066856_A_C 0/0:109,0:0:109:0|1:89066856_A_C | |
| chr2 89066860 . G A . clustered_events;t_lod_fstar ClippingRankSum=0;DP=238;ECNT=2;FS=16.435;HCNT=14;MAX_ED=4;MIN_ED=4;MQ=59.08;MQ0=1;MQRankSum=-11.332;NLOD=27.69;ReadPosRankSum=-1.77;TLOD=4.96;ANN=A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|1/14|n.329+1147G>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000421951|processed_transcript|1/3|n.390+1147G>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000427055|processed_transcript|1/1|n.316+1147G>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|1/16|n.295+1147G>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000443770|processed_transcript|1/2|n.254+1147G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|AC096579.1|ENSG00000221686|transcript|ENST00000408759|miRNA|1/1|n.26G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:120,4:0.027:124:0|1:89066856_A_C 0/0:108,0:0:108:0|1:89066856_A_C | |
| chr2 89102392 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=584;ECNT=3;FS=3.282;HCNT=8;MAX_ED=72;MIN_ED=10;MQ=59.31;MQ0=10;MQRankSum=-13.034;NLOD=25.15;ReadPosRankSum=0.167;TLOD=6.42;ANN=A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|13/16|n.1263-1502C>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000575193|transcribed_unprocessed_pseudogene|12/14|n.1055+10C>A||||||,A|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000454490|retained_intron|1/2|n.377-1502C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|13/15|n.2866C>A|||||| GT:AD:AF:DP:PGT:PID 0/1:396,3:0.012:399:0|1:89102392_C_A 0/0:171,3:0.023:174:0|1:89102392_C_A | |
| chr2 89102402 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=596;ECNT=3;FS=6.734;HCNT=8;MAX_ED=72;MIN_ED=10;MQ=58.82;MQ0=16;MQRankSum=-12.268;NLOD=7.23;ReadPosRankSum=-1.582;TLOD=8.62;ANN=T|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|13/16|n.1263-1492C>T||||||,T|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000575193|transcribed_unprocessed_pseudogene|12/14|n.1055+20C>T||||||,T|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000454490|retained_intron|1/2|n.377-1492C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|13/15|n.2876C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:397,4:0.019:401:0|1:89102392_C_A 0/0:169,6:0.061:175:0|1:89102392_C_A | |
| chr2 89102464 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=440;ECNT=3;FS=1.752;HCNT=12;MAX_ED=72;MIN_ED=10;MQ=56.87;MQ0=13;MQRankSum=-11.966;NLOD=15.53;ReadPosRankSum=2.845;TLOD=5.92;ANN=G|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|13/16|n.1263-1430A>G||||||,G|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000575193|transcribed_unprocessed_pseudogene|12/14|n.1055+82A>G||||||,G|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000454490|retained_intron|1/2|n.377-1430A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|13/15|n.2938A>G|||||| GT:AD:AF:DP 0/1:258,10:0.026:268 0/0:127,6:0.041:133 | |
| chr2 89104928 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=991;ECNT=2;FS=1.163;HCNT=20;MAX_ED=75;MIN_ED=75;MQ=54.1;MQ0=88;MQRankSum=-13.025;NLOD=4.49;ReadPosRankSum=-5.808;TLOD=10.20;ANN=C|splice_region_variant&intron_variant|LOW|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|14/14|n.4898+6T>C||||||,C|splice_region_variant&intron_variant|LOW|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|16/16|n.1457+6T>C||||||,C|downstream_gene_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000575193|transcribed_unprocessed_pseudogene||n.*11T>C|||||11|,C|non_coding_transcript_exon_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000454490|retained_intron|3/3|n.913T>C|||||| GT:AD:AF:DP 0/1:532,14:0.027:546 0/0:229,36:0.127:265 | |
| chr2 89105003 . A T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=981;ECNT=2;FS=1.61;HCNT=14;MAX_ED=75;MIN_ED=75;MQ=52.41;MQ0=105;MQRankSum=-11.588;NLOD=35.28;ReadPosRankSum=2.251;TLOD=14.18;ANN=T|downstream_gene_variant|MODIFIER|AC096579.13|ENSG00000240040|transcript|ENST00000452230|processed_transcript||n.*4981T>A|||||4981|,T|downstream_gene_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000575193|transcribed_unprocessed_pseudogene||n.*86A>T|||||86|,T|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393525|processed_transcript|14/14|n.4898+81A>T||||||,T|intron_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000393515|processed_transcript|16/16|n.1457+81A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD36BP2|ENSG00000230006|transcript|ENST00000454490|retained_intron|3/3|n.988A>T|||||| GT:AD:AF:DP 0/1:451,10:0.02:461 0/0:276,16:0.046:292 | |
| chr2 90259776 . G A . germline_risk ClippingRankSum=0;DP=191;ECNT=1;FS=3.124;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=59.18;MQ0=0;MQRankSum=-8.712;NLOD=1.57;ReadPosRankSum=-3.145;TLOD=45.96;ANN=A|start_lost|HIGH|IGKV1D-8|ENSG00000239819|transcript|ENST00000471857|IG_V_gene|1/2|c.3G>A|p.Met1?|184/532|3/351|1/116||WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(IGKV1D-8|ENSG00000239819|1|1.00) GT:AD:AF:DP 0/1:106,18:0.152:124 0/0:64,3:0.064:67 | |
| chr2 90414077 . T A . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=120;ECNT=5;FS=0;HCNT=11;MAX_ED=45;MIN_ED=20;MQ=46.64;MQ0=2;MQRankSum=-0.32;NLOD=5.12;ReadPosRankSum=-0.923;TLOD=8.81;ANN=A|intergenic_region|MODIFIER|AC113612.1-CH17-132F21.1|ENSG00000234047-ENSG00000270999|intergenic_region|ENSG00000234047-ENSG00000270999|||n.90414077T>A|||||| GT:AD:AF:DP 0/1:54,5:0.077:59 0/0:24,0:0:24 | |
| chr2 90414097 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=142;ECNT=5;FS=0;HCNT=13;MAX_ED=45;MIN_ED=20;MQ=45.88;MQ0=7;MQRankSum=-0.861;NLOD=4.45;ReadPosRankSum=1.834;TLOD=8.52;ANN=A|intergenic_region|MODIFIER|AC113612.1-CH17-132F21.1|ENSG00000234047-ENSG00000270999|intergenic_region|ENSG00000234047-ENSG00000270999|||n.90414097G>A|||||| GT:AD:AF:DP 0/1:69,4:0.058:73 0/0:36,3:0.071:39 | |
| chr2 90414108 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=163;ECNT=5;FS=1.312;HCNT=21;MAX_ED=45;MIN_ED=20;MQ=45.66;MQ0=9;MQRankSum=-1.605;NLOD=8.13;ReadPosRankSum=1.874;TLOD=18.54;ANN=T|intergenic_region|MODIFIER|AC113612.1-CH17-132F21.1|ENSG00000234047-ENSG00000270999|intergenic_region|ENSG00000234047-ENSG00000270999|||n.90414108C>T|||||| GT:AD:AF:DP 0/1:77,9:0.1:86 0/0:41,1:0.034:42 | |
| chr2 90414112 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=170;ECNT=5;FS=1.885;HCNT=10;MAX_ED=45;MIN_ED=20;MQ=45.43;MQ0=9;MQRankSum=-1.91;NLOD=8.43;ReadPosRankSum=1.071;TLOD=8.33;ANN=A|intergenic_region|MODIFIER|AC113612.1-CH17-132F21.1|ENSG00000234047-ENSG00000270999|intergenic_region|ENSG00000234047-ENSG00000270999|||n.90414112G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:87,4:0.05:91:0|1:90414112_G_A 0/0:41,1:0.033:42:0|1:90414112_G_A | |
| chr2 90414122 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=187;ECNT=5;FS=3.938;HCNT=10;MAX_ED=45;MIN_ED=20;MQ=44.84;MQ0=10;MQRankSum=-1.808;NLOD=9.03;ReadPosRankSum=0.867;TLOD=8.18;ANN=C|intergenic_region|MODIFIER|AC113612.1-CH17-132F21.1|ENSG00000234047-ENSG00000270999|intergenic_region|ENSG00000234047-ENSG00000270999|||n.90414122G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:96,4:0.045:100:0|1:90414112_G_A 0/0:44,1:0.03:45:0|1:90414112_G_A | |
| chr2 91712815 . G C . PASS ClippingRankSum=0;DP=1883;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=36.17;MQ0=1089;MQRankSum=0.027;NLOD=21.57;ReadPosRankSum=-0.57;TLOD=13.86;ANN=C|intergenic_region|MODIFIER|AC018696.2-AC018696.5|ENSG00000203344-ENSG00000214164|intergenic_region|ENSG00000203344-ENSG00000214164|||n.91712815G>C|||||| GT:AD:AF:DP 0/1:144,8:0.052:152 0/0:597,32:0.051:629 | |
| chr2 91766609 . G A . PASS ClippingRankSum=0;DP=1066;ECNT=1;FS=0;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=57.56;MQ0=3;MQRankSum=-1.803;NLOD=21.74;ReadPosRankSum=1.016;TLOD=20.52;ANN=A|upstream_gene_variant|MODIFIER|RP11-575H3.1|ENSG00000261600|transcript|ENST00000567067|lincRNA||n.-1784G>A|||||1784|,A|non_coding_transcript_exon_variant|MODIFIER|AC018696.4|ENSG00000230964|transcript|ENST00000454518|processed_pseudogene|1/1|n.73G>A|||||| GT:AD:AF:DP 0/1:638,26:0.034:664 0/0:363,22:0.065:385 | |
| chr2 91777703 . A G . clustered_events;germline_risk ClippingRankSum=0;DP=42;ECNT=2;FS=1.481;HCNT=2;MAX_ED=15;MIN_ED=15;MQ=54.75;MQ0=0;MQRankSum=-4.062;NLOD=1.51;ReadPosRankSum=1.167;TLOD=31.18;ANN=G|non_coding_transcript_exon_variant|MODIFIER|AC116050.1|ENSG00000233991|transcript|ENST00000443031|unprocessed_pseudogene|1/5|n.168A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:22,10:0.357:32:0|1:91777703_A_G 0/0:7,0:0:7:0|1:91777703_A_G | |
| chr2 91777718 . C T . clustered_events;germline_risk ClippingRankSum=0;DP=53;ECNT=2;FS=3.066;HCNT=2;MAX_ED=15;MIN_ED=15;MQ=54.27;MQ0=0;MQRankSum=-4.418;NLOD=2.11;ReadPosRankSum=1.68;TLOD=28.78;ANN=T|non_coding_transcript_exon_variant|MODIFIER|AC116050.1|ENSG00000233991|transcript|ENST00000443031|unprocessed_pseudogene|1/5|n.183C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:28,11:0.31:39:0|1:91777703_A_G 0/0:10,0:0:10:0|1:91777703_A_G | |
| chr2 91842903 . G A . PASS ClippingRankSum=0;DP=522;ECNT=1;FS=12.805;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=47.21;MQ0=83;MQRankSum=-1.858;NLOD=3.92;ReadPosRankSum=-6.04;TLOD=12.68;ANN=A|downstream_gene_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000423774|transcribed_unprocessed_pseudogene||n.*38C>T|||||38|,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000609777|processed_transcript|2/2|n.199+491C>T||||||,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608501|processed_transcript|2/2|n.156+491C>T||||||,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000544283|processed_transcript|3/3|n.386+43C>T||||||,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000271699|transcribed_unprocessed_pseudogene|3/3|n.254+43C>T||||||,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608018|processed_transcript|2/2|n.89+43C>T||||||,A|intron_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608531|processed_transcript|3/3|n.227+43C>T|||||| GT:AD:AF:DP 0/1:243,10:0.049:253 0/0:156,9:0.067:165 | |
| chr2 91843433 . T C . PASS ClippingRankSum=0;DP=137;ECNT=1;FS=7.666;HCNT=44;MAX_ED=.;MIN_ED=.;MQ=54.16;MQ0=16;MQRankSum=-5.527;NLOD=3.65;ReadPosRankSum=-0.212;TLOD=8.78;ANN=C|upstream_gene_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608018|processed_transcript||n.-29A>G|||||29|,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000609777|processed_transcript|2/3|n.160A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608501|processed_transcript|2/3|n.117A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000544283|processed_transcript|2/4|n.269A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000271699|transcribed_unprocessed_pseudogene|2/4|n.137A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000608531|processed_transcript|2/4|n.110A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC027612.6|ENSG00000143429|transcript|ENST00000423774|transcribed_unprocessed_pseudogene|1/2|n.97A>G|||||| GT:AD:AF:DP 0/1:71,6:0.103:77 0/0:31,9:0.258:40 | |
| chr2 91872876 . A G . t_lod_fstar ClippingRankSum=0;DP=248;ECNT=1;FS=27.732;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=50.6;MQ0=14;MQRankSum=0.751;NLOD=10.76;ReadPosRankSum=-1.322;TLOD=4.06;ANN=G|downstream_gene_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000541904|processed_pseudogene||n.*272T>C|||||272|,G|downstream_gene_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000328341|processed_pseudogene||n.*462T>C|||||462|,G|downstream_gene_variant|MODIFIER|AC027612.3|ENSG00000230572|transcript|ENST00000436174|processed_transcript||n.*1252T>C|||||1252|,G|non_coding_transcript_exon_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000456605|processed_pseudogene|1/1|n.1035T>C|||||| GT:AD:AF:DP 0/1:151,3:0.027:154 0/0:67,7:0.123:74 | |
| chr2 91873204 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=208;ECNT=2;FS=15.383;HCNT=18;MAX_ED=68;MIN_ED=68;MQ=47.82;MQ0=12;MQRankSum=0.362;NLOD=0.764;ReadPosRankSum=-4.023;TLOD=12.52;ANN=T|downstream_gene_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000328341|processed_pseudogene||n.*134G>A|||||134|,T|downstream_gene_variant|MODIFIER|AC027612.3|ENSG00000230572|transcript|ENST00000436174|processed_transcript||n.*924G>A|||||924|,T|non_coding_transcript_exon_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000456605|processed_pseudogene|1/1|n.707G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000541904|processed_pseudogene|2/2|n.1125G>A|||||| GT:AD:AF:DP 0/1:130,7:0.074:137 0/0:47,8:0.163:55 | |
| chr2 91873272 . G A . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=282;ECNT=2;FS=1.778;HCNT=15;MAX_ED=68;MIN_ED=68;MQ=41.8;MQ0=83;MQRankSum=3.459;NLOD=1.87;ReadPosRankSum=-1.155;TLOD=5.85;ANN=A|downstream_gene_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000328341|processed_pseudogene||n.*66C>T|||||66|,A|downstream_gene_variant|MODIFIER|AC027612.3|ENSG00000230572|transcript|ENST00000436174|processed_transcript||n.*856C>T|||||856|,A|non_coding_transcript_exon_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000456605|processed_pseudogene|1/1|n.639C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|DRD5P1|ENSG00000184303|transcript|ENST00000541904|processed_pseudogene|2/2|n.1057C>T|||||| GT:AD:AF:DP 0/1:111,4:0.051:115 0/0:61,20:0.279:81 | |
| chr2 92075443 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=398;ECNT=3;FS=5.042;HCNT=3;MAX_ED=10;MIN_ED=6;MQ=57.67;MQ0=2;MQRankSum=-4.363;NLOD=25.90;ReadPosRankSum=1.761;TLOD=6.72;ANN=G|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000398120|transcribed_unprocessed_pseudogene|7/7|n.948+46T>C|||||| GT:AD:AF:DP 0/1:250,3:0.016:253 0/0:137,1:0.009346:138 | |
| chr2 92075449 . A T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=429;ECNT=3;FS=2.577;HCNT=3;MAX_ED=10;MIN_ED=6;MQ=57.87;MQ0=2;MQRankSum=-1.618;NLOD=15.45;ReadPosRankSum=-0.36;TLOD=4.09;ANN=T|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000398120|transcribed_unprocessed_pseudogene|7/7|n.948+40T>A|||||| GT:AD:AF:DP 0/1:273,2:0.009434:275 0/0:141,6:0.044:147 | |
| chr2 92075453 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=451;ECNT=3;FS=5.157;HCNT=6;MAX_ED=10;MIN_ED=6;MQ=58.02;MQ0=2;MQRankSum=-4.483;NLOD=11.25;ReadPosRankSum=-0.913;TLOD=12.17;ANN=T|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000398120|transcribed_unprocessed_pseudogene|7/7|n.948+36G>A|||||| GT:AD:AF:DP 0/1:284,5:0.024:289 0/0:149,6:0.053:155 | |
| chr2 92102048 . T C . t_lod_fstar ClippingRankSum=0;DP=1433;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=47.32;MQ0=170;MQRankSum=2.828;NLOD=70.69;ReadPosRankSum=3.134;TLOD=5.47;ANN=C|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000398120|transcribed_unprocessed_pseudogene|3/7|n.448+24A>G||||||,C|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000606405|processed_transcript|1/2|n.167+24A>G|||||| GT:AD:AF:DP 0/1:770,3:0.005682:773 0/0:409,15:0.041:424 | |
| chr2 92118515 . A G . t_lod_fstar ClippingRankSum=0;DP=472;ECNT=1;FS=0;HCNT=28;MAX_ED=.;MIN_ED=.;MQ=59.04;MQ0=1;MQRankSum=-10.645;NLOD=16.88;ReadPosRankSum=-2.6;TLOD=4.67;ANN=G|intron_variant|MODIFIER|SLC9B1P2|ENSG00000214329|transcript|ENST00000398120|transcribed_unprocessed_pseudogene|1/7|n.145-37T>C|||||| GT:AD:AF:DP 0/1:305,5:0.023:310 0/0:141,9:0.049:150 | |
| chr2 95482968 . C G . PASS ClippingRankSum=0;DP=1764;ECNT=1;FS=17.57;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=35.44;MQ0=749;MQRankSum=1.261;NLOD=33.26;ReadPosRankSum=5.656;TLOD=31.90;ANN=G|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000590226|retained_intron|1/2|n.579G>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000432432|processed_transcript|14/15|n.1560G>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000446135|transcribed_unprocessed_pseudogene|14/15|n.1463G>C|||||| GT:AD:AF:DP 0/1:532,28:0.064:560 0/0:368,53:0.11:421 | |
| chr2 95488835 . C T . t_lod_fstar ClippingRankSum=0;DP=980;ECNT=1;FS=10.419;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=50.58;MQ0=29;MQRankSum=-2.353;NLOD=32.76;ReadPosRankSum=2.425;TLOD=4.60;ANN=T|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000432432|processed_transcript|11/14|n.1195-16G>A||||||,T|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000446135|transcribed_unprocessed_pseudogene|11/14|n.1098-16G>A|||||| GT:AD:AF:DP 0/1:657,8:0.019:665 0/0:253,6:0.036:259 | |
| chr2 95515107 . G A . PASS ClippingRankSum=0;DP=537;ECNT=1;FS=16.816;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=58.93;MQ0=2;MQRankSum=-19.256;NLOD=12.45;ReadPosRankSum=-0.847;TLOD=52.50;ANN=A|upstream_gene_variant|MODIFIER|RNU6-1320P|ENSG00000212140|transcript|ENST00000390838|snRNA||n.-2723C>T|||||2723|,A|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000432432|processed_transcript|3/14|n.606-55C>T||||||,A|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000446135|transcribed_unprocessed_pseudogene|3/14|n.500-41C>T|||||| GT:AD:AF:DP 0/1:318,27:0.068:345 0/0:177,8:0.048:185 | |
| chr2 95522692 . C A . t_lod_fstar ClippingRankSum=0;DP=167;ECNT=1;FS=1.768;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=58.46;MQ0=3;MQRankSum=-5.041;NLOD=15.65;ReadPosRankSum=1.512;TLOD=5.02;ANN=A|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000432432|processed_transcript|1/14|n.316+20G>T||||||,A|intron_variant|MODIFIER|ANKRD20A8P|ENSG00000229089|transcript|ENST00000446135|transcribed_unprocessed_pseudogene|1/14|n.203+20G>T|||||| GT:AD:AF:DP 0/1:89,3:0.027:92 0/0:68,2:0.037:70 | |
| chr2 95542418 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=118;ECNT=3;FS=1.357;HCNT=12;MAX_ED=58;MIN_ED=1;MQ=58.42;MQ0=0;MQRankSum=-9.353;NLOD=3.93;ReadPosRankSum=-0.542;TLOD=11.65;ANN=C|synonymous_variant|LOW|TEKT4|ENSG00000163060|transcript|ENST00000295201|protein_coding|6/6|c.1212T>C|p.Ile404Ile|1349/1505|1212/1308|404/435||,C|downstream_gene_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000427593|protein_coding||c.*3677T>C|||||3292|,C|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000568768|processed_transcript|6/7|n.644-3124A>G||||||,C|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000582835|processed_transcript|8/9|n.1153-3121A>G||||||,C|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000597308|transcribed_unprocessed_pseudogene|5/6|n.526-3124A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000468063|retained_intron|6/6|n.2062T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:75,7:0.068:82:0|1:95542418_T_C 0/0:32,2:0.036:34:0|1:95542418_T_C | |
| chr2 95542419 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=120;ECNT=3;FS=1.356;HCNT=12;MAX_ED=58;MIN_ED=1;MQ=58.45;MQ0=0;MQRankSum=-9.436;NLOD=3.63;ReadPosRankSum=-0.279;TLOD=11.65;ANN=A|missense_variant|MODERATE|TEKT4|ENSG00000163060|transcript|ENST00000295201|protein_coding|6/6|c.1213G>A|p.Ala405Thr|1350/1505|1213/1308|405/435||,A|downstream_gene_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000427593|protein_coding||c.*3678G>A|||||3293|,A|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000568768|processed_transcript|6/7|n.644-3125C>T||||||,A|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000582835|processed_transcript|8/9|n.1153-3122C>T||||||,A|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000597308|transcribed_unprocessed_pseudogene|5/6|n.526-3125C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000468063|retained_intron|6/6|n.2063G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:75,7:0.068:82:0|1:95542418_T_C 0/0:34,2:0.037:36:0|1:95542418_T_C | |
| chr2 95542476 . C T . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=137;ECNT=3;FS=2.345;HCNT=11;MAX_ED=58;MIN_ED=1;MQ=58.45;MQ0=0;MQRankSum=-9.081;NLOD=0.895;ReadPosRankSum=0.733;TLOD=8.83;ANN=T|missense_variant|MODERATE|TEKT4|ENSG00000163060|transcript|ENST00000295201|protein_coding|6/6|c.1270C>T|p.Arg424Cys|1407/1505|1270/1308|424/435||,T|downstream_gene_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000427593|protein_coding||c.*3735C>T|||||3350|,T|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000568768|processed_transcript|6/7|n.644-3182G>A||||||,T|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000582835|processed_transcript|8/9|n.1153-3179G>A||||||,T|intron_variant|MODIFIER|AC097374.2|ENSG00000259848|transcript|ENST00000597308|transcribed_unprocessed_pseudogene|5/6|n.526-3182G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|TEKT4|ENSG00000163060|transcript|ENST00000468063|retained_intron|6/6|n.2120C>T|||||| GT:AD:AF:DP 0/1:75,9:0.079:84 0/0:46,5:0.081:51 | |
| chr2 96521150 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=586;ECNT=3;FS=3.909;HCNT=12;MAX_ED=184;MIN_ED=4;MQ=54.51;MQ0=5;MQRankSum=-4.453;NLOD=7.13;ReadPosRankSum=-4.885;TLOD=38.83;ANN=A|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|63/67|c.4859C>T|p.Ala1620Val|4944/5428|4859/5337|1620/1778||,A|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding|54/58|c.2612C>T|p.Ala871Val|3883/4358|2612/3087|871/1028||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding|55/58|c.1940C>T|p.Ala647Val|3946/4403|1940/2397|647/798||WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000531153|retained_intron||n.*606C>T|||||606|,A|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay||c.*80115C>T|||||2056|WARNING_TRANSCRIPT_NO_START_CODON,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000488721|retained_intron|3/4|n.1032C>T|||||| GT:AD:AF:DP 0/1:344,27:0.073:371 0/0:161,14:0.072:175 | |
| chr2 96521154 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=607;ECNT=3;FS=5.016;HCNT=12;MAX_ED=184;MIN_ED=4;MQ=54.06;MQ0=7;MQRankSum=-3.829;NLOD=16.66;ReadPosRankSum=-2.201;TLOD=29.66;ANN=G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|63/67|c.4855G>C|p.Asp1619His|4940/5428|4855/5337|1619/1778||,G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding|54/58|c.2608G>C|p.Asp870His|3879/4358|2608/3087|870/1028||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding|55/58|c.1936G>C|p.Asp646His|3942/4403|1936/2397|646/798||WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000531153|retained_intron||n.*602G>C|||||602|,G|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay||c.*80111G>C|||||2052|WARNING_TRANSCRIPT_NO_START_CODON,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000488721|retained_intron|3/4|n.1028G>C|||||| GT:AD:AF:DP 0/1:363,20:0.057:383 0/0:174,7:0.05:181 | |
| chr2 96521334 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=911;ECNT=3;FS=18.797;HCNT=20;MAX_ED=184;MIN_ED=4;MQ=50;MQ0=10;MQRankSum=-7.149;NLOD=24.57;ReadPosRankSum=-2.597;TLOD=83.13;ANN=C|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|63/67|c.4675A>G|p.Met1559Val|4760/5428|4675/5337|1559/1778||,C|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding|54/58|c.2428A>G|p.Met810Val|3699/4358|2428/3087|810/1028||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding|55/58|c.1756A>G|p.Met586Val|3762/4403|1756/2397|586/798||WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000531153|retained_intron||n.*422A>G|||||422|,C|downstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay||c.*79931A>G|||||1872|WARNING_TRANSCRIPT_NO_START_CODON,C|non_coding_transcript_exon_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000488721|retained_intron|3/4|n.848A>G|||||| GT:AD:AF:DP 0/1:560,52:0.098:612 0/0:238,11:0.047:249 | |
| chr2 96525830 . C T . PASS ClippingRankSum=0;DP=898;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=54.26;MQ0=21;MQRankSum=-1.761;NLOD=34.15;ReadPosRankSum=0.617;TLOD=6.51;ANN=T|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|60/66|c.3683-8G>A||||||,T|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding|51/57|c.1436-8G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding|52/57|c.764-8G>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON,T|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000531153|retained_intron|28/30|n.2241-8G>A||||||,T|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|41/42|c.*1869-8G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000488721|retained_intron||n.-153G>A|||||153| GT:AD:AF:DP 0/1:555,8:0.014:563 0/0:281,11:0.041:292 | |
| chr2 96551974 . A G . PASS ClippingRankSum=0;DP=195;ECNT=1;FS=22.397;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=48.71;MQ0=23;MQRankSum=-1.37;NLOD=9.90;ReadPosRankSum=-1.503;TLOD=7.95;ANN=G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|51/67|c.3080T>C|p.Leu1027Pro|3165/5428|3080/5337|1027/1778||,G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding|42/58|c.833T>C|p.Leu278Pro|2104/4358|833/3087|278/1028||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding|43/58|c.161T>C|p.Leu54Pro|2167/4403|161/2397|54/798||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding|42/51|c.1343T>C|p.Leu448Pro|2085/2560|1343/1818|448/605||WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|33/43|c.*1408T>C|||||49291|WARNING_TRANSCRIPT_NO_START_CODON,G|non_coding_transcript_exon_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000531153|retained_intron|19/31|n.1638T>C|||||| GT:AD:AF:DP 0/1:75,5:0.091:80 0/0:81,5:0.085:86 | |
| chr2 96593042 . G A . t_lod_fstar ClippingRankSum=0;DP=647;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=55.06;MQ0=25;MQRankSum=-2.697;NLOD=29.60;ReadPosRankSum=-1.666;TLOD=4.45;ANN=A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|27/66|c.1867-8C>T||||||,A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|9/42|c.*195-8C>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|26/26|c.*195-8C>T||||||,A|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding||c.-26090C>T|||||65|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding||c.-37456C>T|||||65|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding||c.-14861C>T|||||65|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:382,7:0.016:389 0/0:204,8:0.029:212 | |
| chr2 96593127 . A G . t_lod_fstar ClippingRankSum=0;DP=489;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=56.32;MQ0=17;MQRankSum=-2.565;NLOD=22.17;ReadPosRankSum=-2.701;TLOD=4.15;ANN=G|splice_donor_variant&intron_variant|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|27/66|c.1866+2T>C||||||,G|splice_donor_variant&intron_variant|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|9/42|c.*194+2T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|splice_donor_variant&intron_variant|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|26/26|c.*194+2T>C||||||,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding||c.-26175T>C|||||150|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding||c.-37541T>C|||||150|WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding||c.-14946T>C|||||150|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ANKRD36C|ENSG00000174501|8|0.38) GT:AD:AF:DP 0/1:295,4:0.018:299 0/0:155,6:0.027:161 | |
| chr2 96594767 . A T . PASS ClippingRankSum=0;DP=336;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=56.09;MQ0=8;MQRankSum=-6.496;NLOD=2.48;ReadPosRankSum=-0.756;TLOD=11.57;ANN=T|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding||c.-27815T>A|||||1790|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding||c.-39181T>A|||||1790|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding||c.-16586T>A|||||1790|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|26/66|c.1837+53T>A||||||,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|8/42|c.*165+53T>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|25/26|c.*165+53T>A|||||| GT:AD:AF:DP 0/1:168,9:0.056:177 0/0:91,9:0.08:100 | |
| chr2 96595010 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=771;ECNT=2;FS=4.296;HCNT=5;MAX_ED=72;MIN_ED=72;MQ=45.48;MQ0=68;MQRankSum=0.201;NLOD=31.23;ReadPosRankSum=-1.535;TLOD=5.09;ANN=G|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|25/67|c.1741T>C|p.Ser581Pro|1826/5428|1741/5337|581/1778||,G|3_prime_UTR_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|7/43|c.*69T>C|||||6255|WARNING_TRANSCRIPT_NO_START_CODON,G|3_prime_UTR_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|24/27|c.*69T>C|||||6255|,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding||c.-28058T>C|||||2033|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding||c.-39424T>C|||||2033|WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding||c.-16829T>C|||||2033|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:426,8:0.023:434 0/0:228,12:0.052:240 | |
| chr2 96595082 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=529;ECNT=2;FS=3.646;HCNT=12;MAX_ED=72;MIN_ED=72;MQ=45.29;MQ0=65;MQRankSum=-0.49;NLOD=15.73;ReadPosRankSum=2.555;TLOD=10.62;ANN=G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000420871|protein_coding||c.-28130G>C|||||2105|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000419039|protein_coding||c.-39496G>C|||||2105|WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000295246|protein_coding||c.-16901G>C|||||2105|WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|24/66|c.1736-67G>C||||||,G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|6/42|c.*64-67G>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|23/26|c.*64-67G>C|||||| GT:AD:AF:DP 0/1:287,12:0.036:299 0/0:146,5:0.036:151 | |
| chr2 96601160 . C T . PASS ClippingRankSum=0;DP=229;ECNT=1;FS=1.351;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=42.66;MQ0=38;MQRankSum=0.182;NLOD=14.48;ReadPosRankSum=-0.491;TLOD=7.78;ANN=T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|24/66|c.1735+42G>A||||||,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|6/42|c.*63+42G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|23/26|c.*63+42G>A|||||| GT:AD:AF:DP 0/1:87,5:0.063:92 0/0:78,7:0.071:85 | |
| chr2 96601199 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=401;ECNT=3;FS=6.713;HCNT=16;MAX_ED=246;MIN_ED=39;MQ=42.67;MQ0=51;MQRankSum=-0.8;NLOD=5.67;ReadPosRankSum=-1.282;TLOD=19.32;ANN=A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|24/66|c.1735+3A>T||||||,A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|6/42|c.*63+3A>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|splice_region_variant&intron_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|23/26|c.*63+3A>T|||||| GT:AD:AF:DP 0/1:193,14:0.072:207 0/0:116,8:0.071:124 | |
| chr2 96601238 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=578;ECNT=3;FS=1.255;HCNT=8;MAX_ED=246;MIN_ED=39;MQ=44.01;MQ0=47;MQRankSum=-4.406;NLOD=28.33;ReadPosRankSum=-0.151;TLOD=35.27;ANN=T|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|24/67|c.1699G>A|p.Ala567Thr|1784/5428|1699/5337|567/1778||,T|3_prime_UTR_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|6/43|c.*27G>A|||||27|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|23/27|c.*27G>A|||||27| GT:AD:AF:DP 0/1:310,29:0.081:339 0/0:162,2:0.008403:164 | |
| chr2 96601445 . A T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=418;ECNT=3;FS=0;HCNT=2;MAX_ED=246;MIN_ED=39;MQ=44.96;MQ0=54;MQRankSum=0.639;NLOD=10.07;ReadPosRankSum=-0.509;TLOD=4.80;ANN=T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|22/66|c.1634-53T>A||||||,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|4/42|c.145-53T>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|21/26|c.1561-53T>A|||||| GT:AD:AF:DP 0/1:229,4:0.023:233 0/0:112,6:0.063:118 | |
| chr2 96604606 . C A . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=620;ECNT=2;FS=0.925;HCNT=14;MAX_ED=69;MIN_ED=69;MQ=52.84;MQ0=36;MQRankSum=-3.483;NLOD=2.00;ReadPosRankSum=0.951;TLOD=51.09;ANN=A|missense_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|22/67|c.1604G>T|p.Gly535Val|1689/5428|1604/5337|535/1778||,A|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|4/42|c.144+129G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|21/26|c.1560+129G>T|||||| GT:AD:AF:DP 0/1:342,37:0.107:379 0/0:171,17:0.091:188 | |
| chr2 96604675 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=670;ECNT=2;FS=2.567;HCNT=10;MAX_ED=69;MIN_ED=69;MQ=47.46;MQ0=118;MQRankSum=-0.927;NLOD=1.77;ReadPosRankSum=-1.519;TLOD=23.99;ANN=C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|21/66|c.1561-26A>G||||||,C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|4/42|c.144+60A>G||||||WARNING_TRANSCRIPT_NO_START_CODON,C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|21/26|c.1560+60A>G|||||| GT:AD:AF:DP 0/1:308,17:0.061:325 0/0:188,16:0.08:204 | |
| chr2 96604752 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=590;ECNT=2;FS=0;HCNT=4;MAX_ED=71;MIN_ED=71;MQ=40.06;MQ0=200;MQRankSum=1.211;NLOD=20.67;ReadPosRankSum=0.457;TLOD=4.45;ANN=A|stop_gained|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|21/67|c.1543C>T|p.Gln515*|1628/5428|1543/5337|515/1778||,A|stop_gained|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|4/43|c.127C>T|p.Gln43*|128/2301|127/183|43/60||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|21/27|c.1543C>T|p.Gln515*|1628/1907|1543/1599|515/532||;LOF=(ANKRD36C|ENSG00000174501|8|0.13);NMD=(ANKRD36C|ENSG00000174501|8|0.13) GT:AD:AF:DP 0/1:165,4:0.026:169 0/0:193,11:0.053:204 | |
| chr2 96604823 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=454;ECNT=2;FS=2.834;HCNT=7;MAX_ED=71;MIN_ED=71;MQ=41.69;MQ0=131;MQRankSum=1.114;NLOD=10.70;ReadPosRankSum=-0.71;TLOD=6.35;ANN=G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|20/66|c.1532-60T>C||||||,G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay|3/42|c.116-60T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|20/26|c.1532-60T>C|||||| GT:AD:AF:DP 0/1:150,3:0.027:153 0/0:148,7:0.062:155 | |
| chr2 96610958 . G T . PASS ClippingRankSum=0;DP=989;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=56.31;MQ0=29;MQRankSum=-0.468;NLOD=18.13;ReadPosRankSum=1.097;TLOD=10.74;ANN=T|upstream_gene_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000534304|nonsense_mediated_decay||c.-90C>A|||||89|WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|17/66|c.1363-36C>A||||||,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|17/26|c.1363-36C>A|||||| GT:AD:AF:DP 0/1:664,11:0.02:675 0/0:250,12:0.059:262 | |
| chr2 96616527 . A C . PASS ClippingRankSum=0;DP=475;ECNT=1;FS=13.855;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=51.82;MQ0=12;MQRankSum=-2.235;NLOD=23.68;ReadPosRankSum=-2.387;TLOD=16.22;ANN=C|missense_variant&splice_region_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|16/67|c.1265T>G|p.Val422Gly|1350/5428|1265/5337|422/1778||,C|missense_variant&splice_region_variant|MODERATE|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|16/27|c.1265T>G|p.Val422Gly|1350/1907|1265/1599|422/532|| GT:AD:AF:DP 0/1:289,12:0.05:301 0/0:149,4:0.026:153 | |
| chr2 96617182 . A C . PASS ClippingRankSum=0;DP=506;ECNT=1;FS=2.191;HCNT=25;MAX_ED=.;MIN_ED=.;MQ=55.9;MQ0=3;MQRankSum=-7.594;NLOD=16.28;ReadPosRankSum=1.159;TLOD=35.01;ANN=C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|14/66|c.1204-26T>G||||||,C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|14/26|c.1204-26T>G|||||| GT:AD:AF:DP 0/1:270,33:0.113:303 0/0:167,10:0.058:177 | |
| chr2 96619687 . C T . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=379;ECNT=3;FS=1.229;HCNT=9;MAX_ED=86;MIN_ED=26;MQ=53.16;MQ0=21;MQRankSum=-5.859;NLOD=23.48;ReadPosRankSum=-1.669;TLOD=11.40;ANN=T|splice_region_variant&synonymous_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|14/67|c.1203G>A|p.Glu401Glu|1288/5428|1203/5337|401/1778||,T|splice_region_variant&synonymous_variant|LOW|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|14/27|c.1203G>A|p.Glu401Glu|1288/1907|1203/1599|401/532|| GT:AD:AF:DP 0/1:209,10:0.048:219 0/0:118,0:0:118 | |
| chr2 96619713 . C A . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=379;ECNT=3;FS=1.186;HCNT=7;MAX_ED=86;MIN_ED=26;MQ=53.24;MQ0=19;MQRankSum=-5.806;NLOD=26.43;ReadPosRankSum=0.949;TLOD=10.39;ANN=A|stop_gained|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|14/67|c.1177G>T|p.Glu393*|1262/5428|1177/5337|393/1778||,A|stop_gained|HIGH|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|14/27|c.1177G>T|p.Glu393*|1262/1907|1177/1599|393/532||;LOF=(ANKRD36C|ENSG00000174501|8|0.25);NMD=(ANKRD36C|ENSG00000174501|8|0.25) GT:AD:AF:DP 0/1:202,11:0.046:213 0/0:124,0:0:124 | |
| chr2 96619773 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=330;ECNT=3;FS=2.196;HCNT=9;MAX_ED=86;MIN_ED=26;MQ=52.54;MQ0=11;MQRankSum=-2.953;NLOD=14.54;ReadPosRankSum=1.596;TLOD=8.48;ANN=C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|13/66|c.1137-20T>G||||||,C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|13/26|c.1137-20T>G|||||| GT:AD:AF:DP 0/1:179,12:0.056:191 0/0:105,3:0.039:108 | |
| chr2 96622460 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=260;ECNT=3;FS=4.645;HCNT=13;MAX_ED=8;MIN_ED=7;MQ=58.68;MQ0=3;MQRankSum=-9.888;NLOD=7.56;ReadPosRankSum=-2.694;TLOD=4.64;ANN=C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|13/66|c.1136+74A>G||||||,C|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|13/26|c.1136+74A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:167,4:0.018:171:0|1:96622460_T_C 0/0:75,6:0.07:81:0|1:96622460_T_C | |
| chr2 96622467 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=264;ECNT=3;FS=2.846;HCNT=13;MAX_ED=8;MIN_ED=7;MQ=58.93;MQ0=3;MQRankSum=-10.008;NLOD=7.56;ReadPosRankSum=-3.428;TLOD=4.62;ANN=A|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|13/66|c.1136+67C>T||||||,A|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|13/26|c.1136+67C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:173,4:0.017:177:0|1:96622460_T_C 0/0:75,6:0.07:81:0|1:96622460_T_C | |
| chr2 96622468 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=264;ECNT=3;FS=2.846;HCNT=13;MAX_ED=8;MIN_ED=7;MQ=58.93;MQ0=3;MQRankSum=-10.008;NLOD=7.25;ReadPosRankSum=-3.551;TLOD=4.62;ANN=T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000456556|protein_coding|13/66|c.1136+66G>A||||||,T|intron_variant|MODIFIER|ANKRD36C|ENSG00000174501|transcript|ENST00000528268|nonsense_mediated_decay|13/26|c.1136+66G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:173,4:0.017:177:0|1:96622460_T_C 0/0:75,6:0.071:81:0|1:96622460_T_C | |
| chr2 96919780 . ATGC A . t_lod_fstar ClippingRankSum=0;DP=149;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.62;ReadPosRankSum=-0.406;TLOD=5.03;ANN=A|disruptive_inframe_deletion|MODERATE|TMEM127|ENSG00000135956|transcript|ENST00000258439|protein_coding|4/4|c.480_482delGCA|p.Gln160del|739/6266|480/717|160/238||,A|disruptive_inframe_deletion|MODERATE|TMEM127|ENSG00000135956|transcript|ENST00000432959|protein_coding|4/4|c.480_482delGCA|p.Gln160del|716/3099|480/717|160/238||,A|disruptive_inframe_deletion|MODERATE|TMEM127|ENSG00000135956|transcript|ENST00000435268|protein_coding|3/3|c.228_230delGCA|p.Gln76del|339/582|228/465|76/154|| GT:AD:AF:DP 0/1:109,3:0.028:112 0/0:33,0:0:33 | |
| chr2 97297146 . G A . t_lod_fstar ClippingRankSum=0;DP=119;ECNT=1;FS=0;HCNT=67;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.81;ReadPosRankSum=-0.277;TLOD=4.99;ANN=A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000431828|protein_coding|3/21|c.289C>T|p.Arg97Cys|366/5153|289/2637|97/878||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000447759|nonsense_mediated_decay|1/22|c.76C>T|p.Arg26Cys|76/5012|76/282|26/93||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000420155|nonsense_mediated_decay|3/21|c.289C>T|p.Arg97Cys|388/5028|289/2343|97/780||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000599854|protein_coding|3/21|c.28C>T|p.Arg10Cys|496/5253|28/2376|10/791||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000441706|protein_coding|3/17|c.28C>T|p.Arg10Cys|435/2000|28/1593|10/530||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000597150|nonsense_mediated_decay|3/21|c.289C>T|p.Arg97Cys|377/2811|289/465|97/154||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000444759|nonsense_mediated_decay|3/20|c.289C>T|p.Arg97Cys|435/2717|289/465|97/154||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000451819|nonsense_mediated_decay|2/4|c.289C>T|p.Arg97Cys|346/693|289/399|97/132||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000418735|nonsense_mediated_decay|2/5|c.28C>T|p.Arg10Cys|119/594|28/204|10/67||,A|missense_variant|MODERATE|KANSL3|ENSG00000114982|transcript|ENST00000435669|protein_coding|3/6|c.28C>T|p.Arg10Cys|373/771|28/426|10/141||,A|5_prime_UTR_premature_start_codon_gain_variant|LOW|KANSL3|ENSG00000114982|transcript|ENST00000440133|protein_coding|3/21|c.-239C>T||||||,A|5_prime_UTR_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000440133|protein_coding|3/21|c.-239C>T|||||12006|,A|3_prime_UTR_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000354204|nonsense_mediated_decay|3/21|c.*131C>T|||||131|,A|3_prime_UTR_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000425656|nonsense_mediated_decay|2/11|c.*131C>T|||||131|,A|3_prime_UTR_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000452268|nonsense_mediated_decay|4/12|c.*88C>T|||||2754|,A|intron_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000448075|protein_coding|1/5|c.-142+6874C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000416138|nonsense_mediated_decay|2/3|c.215+5512C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000487070|processed_transcript|3/20|n.411C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|KANSL3|ENSG00000114982|transcript|ENST00000475820|processed_transcript|3/3|n.512C>T|||||| GT:AD:AF:DP 0/1:93,5:0.041:98 0/0:19,0:0:19 | |
| chr2 97691881 . T A . PASS ClippingRankSum=0;DP=915;ECNT=1;FS=5.172;HCNT=23;MAX_ED=.;MIN_ED=.;MQ=57.17;MQ0=42;MQRankSum=-4.287;NLOD=25.33;ReadPosRankSum=-8.111;TLOD=6.55;ANN=A|non_coding_transcript_exon_variant|MODIFIER|TRIM43CP|ENSG00000144188|transcript|ENST00000422468|unprocessed_pseudogene|5/5|n.865A>T|||||| GT:AD:AF:DP 0/1:566,10:0.017:576 0/0:240,35:0.129:275 | |
| chr2 97693966 . A AG . PASS ClippingRankSum=0;DP=255;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=58.64;MQ0=2;MQRankSum=0.535;NLOD=3.62;ReadPosRankSum=-2.907;TLOD=9.56;ANN=AG|intron_variant|MODIFIER|TRIM43CP|ENSG00000144188|transcript|ENST00000422468|unprocessed_pseudogene|3/4|n.445-566_445-565insC|||||| GT:AD:AF:DP 0/1:38,10:0.08:48 0/0:36,1:0.037:37 | |
| chr2 97749576 . C G . germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=167;ECNT=2;FS=9.316;HCNT=10;MAX_ED=1;MIN_ED=1;MQ=59.32;MQ0=0;MQRankSum=-7.176;NLOD=0.633;ReadPosRankSum=-2.926;TLOD=10.82;ANN=G|downstream_gene_variant|MODIFIER|AC018892.9|ENSG00000188383|transcript|ENST00000340118|unprocessed_pseudogene||n.*1191C>G|||||1191|,G|downstream_gene_variant|MODIFIER|AC018892.9|ENSG00000188383|transcript|ENST00000445404|unprocessed_pseudogene||n.*590C>G|||||590|,G|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000474849|retained_intron||n.*51G>C|||||51|,G|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000463096|retained_intron||n.*91G>C|||||91|,G|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000468548|processed_transcript||n.*2709G>C|||||2709|,G|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000272610|protein_coding|7/7|c.883-22G>C||||||,G|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000414820|protein_coding|8/8|c.883-22G>C||||||,G|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000440566|protein_coding|6/6|c.883-22G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:114,5:0.043:119:0|1:97749576_C_G 0/0:45,2:0.063:47:0|1:97749576_C_G | |
| chr2 97749577 . G A . germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=171;ECNT=2;FS=12.045;HCNT=10;MAX_ED=1;MIN_ED=1;MQ=59.33;MQ0=0;MQRankSum=-7.267;NLOD=0.633;ReadPosRankSum=-2.926;TLOD=10.82;ANN=A|downstream_gene_variant|MODIFIER|AC018892.9|ENSG00000188383|transcript|ENST00000340118|unprocessed_pseudogene||n.*1192G>A|||||1192|,A|downstream_gene_variant|MODIFIER|AC018892.9|ENSG00000188383|transcript|ENST00000445404|unprocessed_pseudogene||n.*591G>A|||||591|,A|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000474849|retained_intron||n.*50C>T|||||50|,A|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000463096|retained_intron||n.*90C>T|||||90|,A|downstream_gene_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000468548|processed_transcript||n.*2708C>T|||||2708|,A|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000272610|protein_coding|7/7|c.883-23C>T||||||,A|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000414820|protein_coding|8/8|c.883-23C>T||||||,A|intron_variant|MODIFIER|FAHD2B|ENSG00000144199|transcript|ENST00000440566|protein_coding|6/6|c.883-23C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:118,5:0.043:123:0|1:97749576_C_G 0/0:45,2:0.063:47:0|1:97749576_C_G | |
| chr2 97790211 . A T . PASS ClippingRankSum=0;DP=412;ECNT=1;FS=35.77;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=54.8;MQ0=13;MQRankSum=-5.923;NLOD=19.58;ReadPosRankSum=-2.339;TLOD=21.91;ANN=T|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|5/76|c.608A>T|p.His203Leu|852/6269|608/5826|203/1941||,T|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|5/75|c.608A>T|p.His203Leu|852/6102|608/5826|203/1941|| GT:AD:AF:DP 0/1:254,14:0.073:268 0/0:121,5:0.033:126 | |
| chr2 97792874 . A G . PASS ClippingRankSum=0;DP=531;ECNT=1;FS=1.655;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=55.88;MQ0=23;MQRankSum=-5.333;NLOD=20.20;ReadPosRankSum=-1.991;TLOD=7.46;ANN=G|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|6/75|c.799+3A>G||||||,G|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|6/74|c.799+3A>G|||||| GT:AD:AF:DP 0/1:317,10:0.032:327 0/0:161,8:0.042:169 | |
| chr2 97808427 . T C . PASS ClippingRankSum=0;DP=467;ECNT=1;FS=3.176;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=49.91;MQ0=28;MQRankSum=-1.545;NLOD=5.53;ReadPosRankSum=1.931;TLOD=6.34;ANN=C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|7/75|c.828+22T>C||||||,C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|7/74|c.828+22T>C|||||| GT:AD:AF:DP 0/1:230,8:0.031:238 0/0:136,10:0.07:146 | |
| chr2 97817590 . T G . PASS ClippingRankSum=0;DP=422;ECNT=1;FS=5.217;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=46.8;MQ0=4;MQRankSum=0.939;NLOD=4.98;ReadPosRankSum=-3.046;TLOD=11.39;ANN=G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|12/75|c.1102-26T>G||||||,G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|12/74|c.1102-26T>G|||||| GT:AD:AF:DP 0/1:243,13:0.049:256 0/0:116,12:0.085:128 | |
| chr2 97820369 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=143;ECNT=3;FS=1.844;HCNT=4;MAX_ED=24;MIN_ED=23;MQ=59.31;MQ0=0;MQRankSum=-7.81;NLOD=10.54;ReadPosRankSum=-0.701;TLOD=6.60;ANN=A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|14/75|c.1194-43G>A||||||,A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|14/74|c.1194-43G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:87,3:0.046:90:0|1:97820369_G_A 0/0:49,2:0.028:51:0|1:97820369_G_A | |
| chr2 97820392 . A T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=162;ECNT=3;FS=3.929;HCNT=8;MAX_ED=24;MIN_ED=23;MQ=59.63;MQ0=0;MQRankSum=-7.187;NLOD=11.13;ReadPosRankSum=-2.852;TLOD=7.27;ANN=T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|14/75|c.1194-20A>T||||||,T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|14/74|c.1194-20A>T|||||| GT:AD:AF:DP 0/1:96,4:0.045:100 0/0:59,2:0.026:61 | |
| chr2 97820393 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=162;ECNT=3;FS=4.978;HCNT=4;MAX_ED=24;MIN_ED=23;MQ=59.63;MQ0=0;MQRankSum=-8.86;NLOD=11.14;ReadPosRankSum=-2.145;TLOD=5.07;ANN=G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|14/75|c.1194-19A>G||||||,G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|14/74|c.1194-19A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:98,2:0.029:100:0|1:97820369_G_A 0/0:59,2:0.026:61:0|1:97820369_G_A | |
| chr2 97827908 . C A . PASS ClippingRankSum=0;DP=399;ECNT=1;FS=3.881;HCNT=5;MAX_ED=.;MIN_ED=.;MQ=49.33;MQ0=4;MQRankSum=-2.078;NLOD=13.99;ReadPosRankSum=0.734;TLOD=6.37;ANN=A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|18/75|c.1429+33C>A||||||,A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|18/74|c.1429+33C>A|||||| GT:AD:AF:DP 0/1:274,5:0.024:279 0/0:76,1:0.017:77 | |
| chr2 97829960 . T C . PASS ClippingRankSum=0;DP=559;ECNT=1;FS=0.693;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=40.27;MQ0=169;MQRankSum=-0.075;NLOD=2.22;ReadPosRankSum=2.27;TLOD=13.03;ANN=C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|18/75|c.1430-60T>C||||||,C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|18/74|c.1430-60T>C|||||| GT:AD:AF:DP 0/1:176,13:0.064:189 0/0:159,19:0.101:178 | |
| chr2 97830031 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=655;ECNT=4;FS=0;HCNT=9;MAX_ED=148;MIN_ED=73;MQ=38.4;MQ0=218;MQRankSum=-0.228;NLOD=19.53;ReadPosRankSum=-0.16;TLOD=9.10;ANN=T|stop_gained|HIGH|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|19/76|c.1441C>T|p.Gln481*|1685/6269|1441/5826|481/1941||,T|stop_gained|HIGH|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|19/75|c.1441C>T|p.Gln481*|1685/6102|1441/5826|481/1941||;LOF=(ANKRD36|ENSG00000135976|6|0.33);NMD=(ANKRD36|ENSG00000135976|6|0.33) GT:AD:AF:DP 0/1:193,11:0.046:204 0/0:186,13:0.057:199 | |
| chr2 97830104 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=521;ECNT=4;FS=0.967;HCNT=11;MAX_ED=148;MIN_ED=73;MQ=44.9;MQ0=115;MQRankSum=-2.856;NLOD=10.50;ReadPosRankSum=1.83;TLOD=10.84;ANN=C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|19/75|c.1459-30G>C||||||,C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|19/74|c.1459-30G>C|||||| GT:AD:AF:DP 0/1:173,10:0.06:183 0/0:94,6:0.082:100 | |
| chr2 97830108 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=511;ECNT=4;FS=0;HCNT=14;MAX_ED=148;MIN_ED=73;MQ=45.11;MQ0=113;MQRankSum=-2.208;NLOD=9.99;ReadPosRankSum=1.38;TLOD=11.73;ANN=G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|19/75|c.1459-26A>G||||||,G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|19/74|c.1459-26A>G|||||| GT:AD:AF:DP 0/1:231,9:0.048:240 0/0:131,6:0.049:137 | |
| chr2 97830179 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=258;ECNT=4;FS=3.467;HCNT=9;MAX_ED=148;MIN_ED=73;MQ=53.78;MQ0=33;MQRankSum=-3.782;NLOD=4.68;ReadPosRankSum=-4.846;TLOD=9.16;ANN=A|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|20/76|c.1504G>A|p.Gly502Ser|1748/6269|1504/5826|502/1941||,A|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|20/75|c.1504G>A|p.Gly502Ser|1748/6102|1504/5826|502/1941|| GT:AD:AF:DP 0/1:136,7:0.065:143 0/0:52,11:0.196:63 | |
| chr2 97833261 . T A . PASS ClippingRankSum=0;DP=732;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=46.93;MQ0=18;MQRankSum=-2.578;NLOD=12.16;ReadPosRankSum=1.278;TLOD=31.78;ANN=A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|20/75|c.1532-53T>A||||||,A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|20/74|c.1532-53T>A|||||| GT:AD:AF:DP 0/1:447,35:0.067:482 0/0:169,10:0.044:179 | |
| chr2 97833507 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=416;ECNT=2;FS=1.07;HCNT=7;MAX_ED=39;MIN_ED=39;MQ=43.25;MQ0=54;MQRankSum=0.832;NLOD=2.11;ReadPosRankSum=1.247;TLOD=5.84;ANN=T|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|22/75|c.1633+3A>T||||||,T|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|22/74|c.1633+3A>T|||||| GT:AD:AF:DP 0/1:200,6:0.029:206 0/0:118,7:0.069:125 | |
| chr2 97833546 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=376;ECNT=2;FS=13.321;HCNT=6;MAX_ED=39;MIN_ED=39;MQ=45.99;MQ0=27;MQRankSum=-1.052;NLOD=6.82;ReadPosRankSum=-0.939;TLOD=8.33;ANN=A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|22/75|c.1633+42G>A||||||,A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|22/74|c.1633+42G>A|||||| GT:AD:AF:DP 0/1:203,6:0.037:209 0/0:107,3:0.051:110 | |
| chr2 97851015 . T G . PASS ClippingRankSum=0;DP=140;ECNT=1;FS=10.838;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=54.14;MQ0=0;MQRankSum=-4.854;NLOD=12.34;ReadPosRankSum=-3.208;TLOD=9.18;ANN=G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|28/75|c.1940-38T>G||||||,G|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|28/74|c.1940-38T>G|||||| GT:AD:AF:DP 0/1:76,6:0.097:82 0/0:50,0:0:50 | |
| chr2 97851156 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=380;ECNT=4;FS=7.102;HCNT=20;MAX_ED=118;MIN_ED=1;MQ=45.38;MQ0=61;MQRankSum=-3.734;NLOD=20.77;ReadPosRankSum=-1.274;TLOD=16.21;ANN=C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|29/75|c.1969-19T>C||||||,C|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|29/74|c.1969-19T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:193,8:0.042:201:0|1:97851156_T_C 0/0:93,1:0.014:94:0|1:97851156_T_C | |
| chr2 97851157 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=383;ECNT=4;FS=7.2;HCNT=20;MAX_ED=118;MIN_ED=1;MQ=45.56;MQ0=61;MQRankSum=-3.758;NLOD=20.47;ReadPosRankSum=-1.363;TLOD=16.21;ANN=A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|29/75|c.1969-18G>A||||||,A|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|29/74|c.1969-18G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:195,8:0.042:203:0|1:97851156_T_C 0/0:94,1:0.014:95:0|1:97851156_T_C | |
| chr2 97851200 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=387;ECNT=4;FS=3.456;HCNT=36;MAX_ED=118;MIN_ED=1;MQ=49.28;MQ0=64;MQRankSum=-3.168;NLOD=18.61;ReadPosRankSum=-2.982;TLOD=6.55;ANN=T|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|30/76|c.1994C>T|p.Ala665Val|2238/6269|1994/5826|665/1941||,T|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|30/75|c.1994C>T|p.Ala665Val|2238/6102|1994/5826|665/1941|| GT:AD:AF:DP 0/1:208,5:0.036:213 0/0:93,2:0.031:95 | |
| chr2 97851274 . C T . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=326;ECNT=4;FS=0;HCNT=12;MAX_ED=118;MIN_ED=1;MQ=55.81;MQ0=22;MQRankSum=-5.006;NLOD=8.64;ReadPosRankSum=-0.965;TLOD=6.05;ANN=T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|30/75|c.2041+27C>T||||||,T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|30/74|c.2041+27C>T|||||| GT:AD:AF:DP 0/1:205,5:0.027:210 0/0:83,3:0.048:86 | |
| chr2 97915895 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1420;ECNT=4;FS=20.25;HCNT=18;MAX_ED=89;MIN_ED=1;MQ=28.87;MQ0=990;MQRankSum=4.768;NLOD=3.03;ReadPosRankSum=3.499;TLOD=13.25;ANN=C|synonymous_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|75/76|c.5817T>C|p.Phe1939Phe|6061/6269|5817/5826|1939/1941||,C|synonymous_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|75/75|c.5817T>C|p.Phe1939Phe|6061/6102|5817/5826|1939/1941||,C|3_prime_UTR_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000357042|protein_coding|4/5|c.*103T>C|||||601|,C|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000421946|retained_intron||n.*1108T>C|||||1108|,C|non_coding_transcript_exon_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000494336|retained_intron|4/4|n.1142T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:96,5:0.049:101:0|1:97915895_T_C 0/0:217,92:0.283:309:0|1:97915895_T_C | |
| chr2 97915896 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1418;ECNT=4;FS=20.25;HCNT=18;MAX_ED=89;MIN_ED=1;MQ=28.98;MQ0=986;MQRankSum=4.803;NLOD=3.03;ReadPosRankSum=3.439;TLOD=13.25;ANN=A|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|75/76|c.5818G>A|p.Glu1940Lys|6062/6269|5818/5826|1940/1941||,A|missense_variant|MODERATE|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|75/75|c.5818G>A|p.Glu1940Lys|6062/6102|5818/5826|1940/1941||,A|3_prime_UTR_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000357042|protein_coding|4/5|c.*104G>A|||||602|,A|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000421946|retained_intron||n.*1109G>A|||||1109|,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000494336|retained_intron|4/4|n.1143G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:98,5:0.049:103:0|1:97915895_T_C 0/0:219,92:0.286:311:0|1:97915895_T_C | |
| chr2 97915916 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=1430;ECNT=4;FS=24.138;HCNT=18;MAX_ED=89;MIN_ED=1;MQ=29.24;MQ0=960;MQRankSum=5.001;NLOD=6.93;ReadPosRankSum=1.887;TLOD=5.13;ANN=C|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|75/75|c.*6+6T>C||||||,C|splice_region_variant&intron_variant|LOW|ANKRD36|ENSG00000135976|transcript|ENST00000357042|protein_coding|4/4|c.*118+6T>C||||||,C|3_prime_UTR_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding|75/75|c.*12T>C|||||12|,C|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000421946|retained_intron||n.*1129T>C|||||1129|,C|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000494336|retained_intron||n.*1T>C|||||1| GT:AD:AF:DP 0/1:133,5:0.036:138 0/0:234,79:0.248:313 | |
| chr2 97915984 . TC T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1384;ECNT=4;FS=17.485;HCNT=22;MAX_ED=89;MIN_ED=1;MQ=33.63;MQ0=610;MQRankSum=4.809;NLOD=12.50;ReadPosRankSum=-5.153;TLOD=10.52;ANN=T|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000461153|protein_coding||c.*81delC|||||49|,T|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000421946|retained_intron||n.*1198delC|||||1198|,T|downstream_gene_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000494336|retained_intron||n.*70delC|||||70|,T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000420699|protein_coding|75/75|c.*6+77delC||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|ANKRD36|ENSG00000135976|transcript|ENST00000357042|protein_coding|4/4|c.*118+77delC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:400,6:0.023:406 0/0:274,40:0.152:314 | |
| chr2 98861944 . T G . clustered_events;t_lod_fstar ClippingRankSum=0;DP=98;ECNT=2;FS=0;HCNT=5;MAX_ED=8;MIN_ED=8;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=0.864;TLOD=4.15;ANN=G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000477737|protein_coding|19/27|c.2674-4837T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000432242|nonsense_mediated_decay|19/28|c.*2427-4837T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000409460|retained_intron|19/22|n.2880-4837T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000495571|nonsense_mediated_decay|10/19|c.*1020-4837T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000489630|nonsense_mediated_decay|6/14|c.*461-4837T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000473149|protein_coding|7/14|c.904-4837T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000465555|protein_coding|2/2|c.138+3183T>G||||||WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000490947|processed_transcript|1/11|n.49T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:65,1:0.036:66:0|1:98861944_T_G 0/0:31,0:0:31:0|1:98861944_T_G | |
| chr2 98861952 . T G . clustered_events;t_lod_fstar ClippingRankSum=0;DP=111;ECNT=2;FS=0;HCNT=5;MAX_ED=8;MIN_ED=8;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.53;ReadPosRankSum=-0.334;TLOD=4.09;ANN=G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000477737|protein_coding|19/27|c.2674-4829T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000432242|nonsense_mediated_decay|19/28|c.*2427-4829T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000409460|retained_intron|19/22|n.2880-4829T>G||||||,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000495571|nonsense_mediated_decay|10/19|c.*1020-4829T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000489630|nonsense_mediated_decay|6/14|c.*461-4829T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000473149|protein_coding|7/14|c.904-4829T>G||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000465555|protein_coding|2/2|c.138+3191T>G||||||WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|VWA3B|ENSG00000168658|transcript|ENST00000490947|processed_transcript|1/11|n.57T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:76,2:0.034:78:0|1:98861944_T_G 0/0:32,0:0:32:0|1:98861944_T_G | |
| chr2 99156092 . G T . t_lod_fstar ClippingRankSum=0;DP=49;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.01;ReadPosRankSum=-0.571;TLOD=4.15;ANN=T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000074304|protein_coding|10/26|c.772G>T|p.Val258Leu|1165/6752|772/2934|258/977||,T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000409016|protein_coding|10/26|c.772G>T|p.Val258Leu|1169/9996|772/2817|258/938||,T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000409851|protein_coding|10/25|c.772G>T|p.Val258Leu|1165/3365|772/2919|258/972||,T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000545415|protein_coding|10/26|c.772G>T|p.Val258Leu|1165/6635|772/2817|258/938||,T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000409540|protein_coding|10/26|c.772G>T|p.Val258Leu|1073/3231|772/2865|258/954||,T|missense_variant|MODERATE|INPP4A|ENSG00000040933|transcript|ENST00000523221|protein_coding|8/24|c.772G>T|p.Val258Leu|772/2934|772/2934|258/977||,T|intron_variant|MODIFIER|INPP4A|ENSG00000040933|transcript|ENST00000409463|protein_coding|5/10|c.231+6173G>T|||||| GT:AD:AF:DP 0/1:30,3:0.091:33 0/0:16,0:0:16 | |
| chr2 99758020 . G GCGCCGGCGCCCGCCCA . germline_risk ClippingRankSum=0;DP=241;ECNT=1;FS=0;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=0;NLOD=2.02;ReadPosRankSum=-0.366;TLOD=31.49;ANN=GCGCCGGCGCCCGCCCA|5_prime_UTR_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000355053|protein_coding|1/20|c.-615_-614insTGGGCGGGCGCCGGCG|||||32119|,GCGCCGGCGCCCGCCCA|5_prime_UTR_variant|MODIFIER|C2ORF15|ENSG00000273045|transcript|ENST00000302513|protein_coding|1/4|c.-561_-560insCGGCGCCCGCCCACGC|||||5907|INFO_REALIGN_3_PRIME,GCGCCGGCGCCCGCCCA|5_prime_UTR_variant|MODIFIER|C2orf15|ENSG00000241962|transcript|ENST00000424491|nonsense_mediated_decay|1/14|c.-561_-560insCGGCGCCCGCCCACGC|||||5907|INFO_REALIGN_3_PRIME,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000539964|protein_coding||c.-32119_-32118insTGGGCGGGCGCCGGCG|||||139|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000393482|protein_coding||c.-32119_-32118insTGGGCGGGCGCCGGCG|||||139|WARNING_TRANSCRIPT_INCOMPLETE,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000542655|protein_coding||c.-32119_-32118insTGGGCGGGCGCCGGCG|||||409|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000489926|processed_transcript||n.-409_-408insTGGGCGGGCGCCGGCG|||||409|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000497915|processed_transcript||n.-378_-377insTGGGCGGGCGCCGGCG|||||378|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000494483|processed_transcript||n.-137_-136insTGGGCGGGCGCCGGCG|||||137|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000462782|retained_intron||n.-137_-136insTGGGCGGGCGCCGGCG|||||137|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000464459|retained_intron||n.-409_-408insTGGGCGGGCGCCGGCG|||||409|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|C2ORF15|ENSG00000273045|transcript|ENST00000409684|protein_coding||c.-5911_-5910insCGCCGGCGCCCGCCCA|||||192|,GCGCCGGCGCCCGCCCA|upstream_gene_variant|MODIFIER|C2ORF15|ENSG00000273045|transcript|ENST00000496794|retained_intron||n.-393_-392insCGCCGGCGCCCGCCCA|||||392|,GCGCCGGCGCCCGCCCA|intron_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000393483|protein_coding|1/20|c.-621+13135_-621+13136insTGGGCGGGCGCCGGCG||||||,GCGCCGGCGCCCGCCCA|intron_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000471174|processed_transcript|1/3|n.270+13135_270+13136insTGGGCGGGCGCCGGCG||||||,GCGCCGGCGCCCGCCCA|intron_variant|MODIFIER|TSGA10|ENSG00000135951|transcript|ENST00000476849|processed_transcript|1/3|n.272+13135_272+13136insTGGGCGGGCGCCGGCG|||||| GT:AD:AF:DP 0/1:135,28:0.25:163 0/0:65,8:nan:73 | |
| chr2 100041269 . G T . t_lod_fstar ClippingRankSum=0;DP=367;ECNT=1;FS=1.69;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=21.36;ReadPosRankSum=1.192;TLOD=4.45;ANN=T|stop_gained|HIGH|REV1|ENSG00000135945|transcript|ENST00000450415|protein_coding|5/5|c.551C>A|p.Ser184*|551/577|551/577|184/191||WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|REV1|ENSG00000135945|transcript|ENST00000481719|retained_intron||n.-173C>A|||||173|,T|intron_variant|MODIFIER|REV1|ENSG00000135945|transcript|ENST00000258428|protein_coding|9/22|c.1548-527C>A||||||,T|intron_variant|MODIFIER|REV1|ENSG00000135945|transcript|ENST00000393445|protein_coding|9/22|c.1545-527C>A||||||,T|intron_variant|MODIFIER|REV1|ENSG00000135945|transcript|ENST00000413697|nonsense_mediated_decay|10/22|c.*1492-527C>A||||||,T|intron_variant|MODIFIER|REV1|ENSG00000135945|transcript|ENST00000465835|processed_transcript|7/17|n.1503-527C>A|||||| GT:AD:AF:DP 0/1:253,5:0.017:258 0/0:108,0:0:108 | |
| chr2 101188260 . G GA . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=143;ECNT=2;FS=6.583;HCNT=32;MAX_ED=2;MIN_ED=2;MQ=58.26;MQ0=0;MQRankSum=-8.42;NLOD=7.85;ReadPosRankSum=-5.785;TLOD=28.88;ANN=GA|frameshift_variant|HIGH|PDCL3|ENSG00000115539|transcript|ENST00000450127|protein_coding|3/3|c.418_419insA|p.Gly140fs|421/662|419/450|140/149||WARNING_TRANSCRIPT_NO_START_CODON,GA|splice_donor_variant&intron_variant|HIGH|PDCL3|ENSG00000115539|transcript|ENST00000264254|protein_coding|5/5|c.577_577+1insA||||||,GA|downstream_gene_variant|MODIFIER|PDCL3|ENSG00000115539|transcript|ENST00000416255|protein_coding||c.*166_*167insA|||||167|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(PDCL3|ENSG00000115539|3|0.67) GT:AD:AF:DP:PGT:PID 0/1:72,11:0.15:83:0|1:101188260_G_GA 0/0:51,2:0.024:53:0|1:101188260_G_GA | |
| chr2 101188262 . T TTGGAATGGA . multi_event_alt_allele_in_normal ClippingRankSum=0;DP=140;ECNT=2;FS=4.737;HCNT=32;MAX_ED=2;MIN_ED=2;MQ=58.4;MQ0=0;MQRankSum=-8.824;NLOD=8.15;ReadPosRankSum=-5.651;TLOD=32.07;ANN=TTGGAATGGA|conservative_inframe_insertion|MODERATE|PDCL3|ENSG00000115539|transcript|ENST00000450127|protein_coding|3/3|c.420_421insTGGAATGGA|p.Gly140_Lys141insTrpAsnGly|423/662|421/450|141/149||WARNING_TRANSCRIPT_NO_START_CODON,TTGGAATGGA|splice_region_variant&intron_variant|LOW|PDCL3|ENSG00000115539|transcript|ENST00000264254|protein_coding|5/5|c.577+2_577+3insTGGAATGGA||||||,TTGGAATGGA|downstream_gene_variant|MODIFIER|PDCL3|ENSG00000115539|transcript|ENST00000416255|protein_coding||c.*168_*169insTGGAATGGA|||||169|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP:PGT:PID 0/1:73,10:0.161:83:0|1:101188260_G_GA 0/0:50,2:0.024:52:0|1:101188260_G_GA | |
| chr2 107041612 . A C . PASS ClippingRankSum=0;DP=1947;ECNT=1;FS=22.592;HCNT=25;MAX_ED=.;MIN_ED=.;MQ=51.18;MQ0=215;MQRankSum=-7.664;NLOD=33.49;ReadPosRankSum=2.645;TLOD=92.91;ANN=C|missense_variant|MODERATE|RGPD3|ENSG00000153165|transcript|ENST00000304514|protein_coding|20/23|c.2811T>G|p.Ser937Arg|2893/5383|2811/5301|937/1766||,C|missense_variant|MODERATE|RGPD3|ENSG00000153165|transcript|ENST00000409886|protein_coding|20/23|c.2811T>G|p.Ser937Arg|2899/5594|2811/5277|937/1758|| GT:AD:AF:DP 0/1:1034,68:0.086:1102 0/0:495,70:0.124:565 | |
| chr2 107052944 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1239;ECNT=2;FS=6.742;HCNT=22;MAX_ED=8;MIN_ED=8;MQ=41.01;MQ0=322;MQRankSum=-0.158;NLOD=38.65;ReadPosRankSum=-2.345;TLOD=26.22;ANN=T|synonymous_variant|LOW|RGPD3|ENSG00000153165|transcript|ENST00000304514|protein_coding|11/23|c.1560G>A|p.Val520Val|1642/5383|1560/5301|520/1766||,T|synonymous_variant|LOW|RGPD3|ENSG00000153165|transcript|ENST00000409886|protein_coding|11/23|c.1560G>A|p.Val520Val|1648/5594|1560/5277|520/1758|| GT:AD:AF:DP:PGT:PID 0/1:452,11:0.03:463:0|1:107052944_C_T 0/0:389,18:0.055:407:0|1:107052944_C_T | |
| chr2 107052952 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1208;ECNT=2;FS=5.689;HCNT=22;MAX_ED=8;MIN_ED=8;MQ=41.74;MQ0=294;MQRankSum=0.896;NLOD=32.28;ReadPosRankSum=-2.372;TLOD=26.21;ANN=A|missense_variant|MODERATE|RGPD3|ENSG00000153165|transcript|ENST00000304514|protein_coding|11/23|c.1552C>T|p.Leu518Phe|1634/5383|1552/5301|518/1766||,A|missense_variant|MODERATE|RGPD3|ENSG00000153165|transcript|ENST00000409886|protein_coding|11/23|c.1552C>T|p.Leu518Phe|1640/5594|1552/5277|518/1758|| GT:AD:AF:DP:PGT:PID 0/1:464,10:0.03:474:0|1:107052944_C_T 0/0:380,22:0.064:402:0|1:107052944_C_T | |
| chr2 108475828 . A G . PASS ClippingRankSum=0;DP=1009;ECNT=1;FS=28.915;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=39.96;MQ0=373;MQRankSum=-7.493;NLOD=15.51;ReadPosRankSum=-4.228;TLOD=49.13;ANN=G|splice_region_variant&intron_variant|LOW|RGPD4|ENSG00000196862|transcript|ENST00000354986|protein_coding|10/22|c.1459-7A>G||||||,G|splice_region_variant&intron_variant|LOW|RGPD4|ENSG00000196862|transcript|ENST00000408999|protein_coding|10/22|c.1459-7A>G|||||| GT:AD:AF:DP 0/1:293,34:0.129:327 0/0:281,10:0.043:291 | |
| chr2 109384167 . C G . t_lod_fstar ClippingRankSum=0;DP=1180;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=55.85;MQ0=20;MQRankSum=-5.701;NLOD=72.83;ReadPosRankSum=-3.396;TLOD=4.51;ANN=G|missense_variant|MODERATE|RANBP2|ENSG00000153201|transcript|ENST00000283195|protein_coding|20/29|c.7172C>G|p.Thr2391Ser|7298/11711|7172/9675|2391/3224|| GT:AD:AF:DP 0/1:778,9:0.016:787 0/0:362,2:0.007519:364 | |
| chr2 110882861 . AT A . t_lod_fstar ClippingRankSum=0;DP=246;ECNT=1;FS=0;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=3.597;NLOD=14.48;ReadPosRankSum=-0.629;TLOD=5.86;ANN=A|frameshift_variant|HIGH|NPHP1|ENSG00000144061|transcript|ENST00000417665|protein_coding|20/21|c.1797delA|p.Lys599fs|1824/2246|1797/2136|599/711||,A|downstream_gene_variant|MODIFIER|AC013268.1|ENSG00000212091|transcript|ENST00000390802|miRNA||n.*1447delA|||||1447|,A|downstream_gene_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000422492|protein_coding||c.*328delA|||||114|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000493051|retained_intron||n.*3667delA|||||3667|,A|intron_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000316534|protein_coding|19/19|c.1929+352delA||||||,A|intron_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000445609|protein_coding|19/19|c.1761+352delA||||||,A|intron_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000393272|protein_coding|19/19|c.1926+352delA||||||,A|intron_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000461707|retained_intron|18/18|n.3346+352delA||||||,A|intron_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000355301|protein_coding|17/17|c.1572+352delA||||||,A|non_coding_transcript_exon_variant|MODIFIER|NPHP1|ENSG00000144061|transcript|ENST00000496524|retained_intron|16/16|n.8069delA||||||;LOF=(NPHP1|ENSG00000144061|11|0.09) GT:AD:AF:DP 0/1:137,16:0.107:153 0/0:74,0:0:74 | |
| chr2 111598173 . G T . t_lod_fstar ClippingRankSum=0;DP=163;ECNT=1;FS=0;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.53;ReadPosRankSum=-0.718;TLOD=6.02;ANN=T|intron_variant|MODIFIER|ACOXL|ENSG00000153093|transcript|ENST00000439055|protein_coding|9/17|c.754-775G>T||||||,T|intron_variant|MODIFIER|ACOXL|ENSG00000153093|transcript|ENST00000389811|protein_coding|9/18|c.754-775G>T||||||,T|intron_variant|MODIFIER|ACOXL|ENSG00000153093|transcript|ENST00000340561|protein_coding|9/10|c.754-775G>T||||||,T|intron_variant|MODIFIER|ACOXL|ENSG00000153093|transcript|ENST00000417074|protein_coding|3/11|c.268-775G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|ACOXL|ENSG00000153093|transcript|ENST00000433706|protein_coding|1/5|c.76-775G>T||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:108,4:0.035:112 0/0:50,0:0:50 | |
| chr2 112849245 . G T . t_lod_fstar ClippingRankSum=0;DP=263;ECNT=1;FS=2.315;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.75;ReadPosRankSum=1.242;TLOD=4.54;ANN=T|intron_variant|MODIFIER|TMEM87B|ENSG00000153214|transcript|ENST00000283206|protein_coding|10/18|c.1033-44G>T||||||,T|intron_variant|MODIFIER|TMEM87B|ENSG00000153214|transcript|ENST00000463427|processed_transcript|2/7|n.176-44G>T||||||,T|intron_variant|MODIFIER|TMEM87B|ENSG00000153214|transcript|ENST00000471632|processed_transcript|1/4|n.88-44G>T|||||| GT:AD:AF:DP 0/1:172,3:0.025:175 0/0:88,0:0:88 | |
| chr2 113127775 . G C . PASS ClippingRankSum=0;DP=415;ECNT=1;FS=91.707;HCNT=21;MAX_ED=.;MIN_ED=.;MQ=49.05;MQ0=3;MQRankSum=-4.864;NLOD=26.46;ReadPosRankSum=-0.934;TLOD=41.43;ANN=C|missense_variant|MODERATE|RGPD8|ENSG00000169629|transcript|ENST00000302558|protein_coding|23/23|c.5278C>G|p.Pro1760Ala|5470/5576|5278/5298|1760/1765||,C|missense_variant|MODERATE|RGPD8|ENSG00000169629|transcript|ENST00000409750|protein_coding|22/22|c.4858C>G|p.Pro1620Ala|5438/5544|4858/4878|1620/1625|| GT:AD:AF:DP 0/1:176,20:0.14:196 0/0:166,7:0.051:173 | |
| chr2 113135356 . T G . PASS ClippingRankSum=0;DP=1502;ECNT=1;FS=11.636;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=34.4;MQ0=674;MQRankSum=-2.529;NLOD=13.87;ReadPosRankSum=-1.911;TLOD=18.51;ANN=G|intron_variant|MODIFIER|RGPD8|ENSG00000169629|transcript|ENST00000302558|protein_coding|22/22|c.5263+274A>C||||||,G|intron_variant|MODIFIER|RGPD8|ENSG00000169629|transcript|ENST00000409750|protein_coding|21/21|c.4843+274A>C|||||| GT:AD:AF:DP 0/1:303,21:0.067:324 0/0:418,25:0.066:443 | |
| chr2 113147223 . C T . PASS ClippingRankSum=0;DP=1087;ECNT=1;FS=10.078;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=36.56;MQ0=395;MQRankSum=-3.027;NLOD=20.40;ReadPosRankSum=-6.951;TLOD=23.20;ANN=T|missense_variant|MODERATE|RGPD8|ENSG00000169629|transcript|ENST00000302558|protein_coding|20/23|c.3299G>A|p.Arg1100Gln|3491/5576|3299/5298|1100/1765||,T|missense_variant|MODERATE|RGPD8|ENSG00000169629|transcript|ENST00000409750|protein_coding|19/22|c.2879G>A|p.Arg960Gln|3459/5544|2879/4878|960/1625||,T|downstream_gene_variant|MODIFIER|RGPD8|ENSG00000169629|transcript|ENST00000522286|nonsense_mediated_decay||c.*22975G>A|||||504|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|RGPD8|ENSG00000169629|transcript|ENST00000330575|protein_coding||c.*3461G>A|||||3405| GT:AD:AF:DP 0/1:332,17:0.061:349 0/0:295,4:0.017:299 | |
| chr2 114257162 . A C . PASS ClippingRankSum=0;DP=523;ECNT=1;FS=14.215;HCNT=21;MAX_ED=.;MIN_ED=.;MQ=50.3;MQ0=34;MQRankSum=-1.515;NLOD=2.89;ReadPosRankSum=-4.185;TLOD=21.33;ANN=C|missense_variant|MODERATE|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.329A>C|p.Tyr110Ser|502/2068|329/1227|110/408||,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*3842A>C|||||3396|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*3842A>C|||||3414|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*3842A>C|||||3414|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*60543A>C|||||3466|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000456188|nonsense_mediated_decay||c.*42500A>C|||||3786|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*3466A>C|||||3466|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*3464A>C|||||3464| GT:AD:AF:DP 0/1:292,18:0.078:310 0/0:150,22:0.121:172 | |
| chr2 114257296 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=551;ECNT=2;FS=6.228;HCNT=22;MAX_ED=58;MIN_ED=58;MQ=51.91;MQ0=8;MQRankSum=-9.119;NLOD=13.15;ReadPosRankSum=-1.438;TLOD=47.62;ANN=G|missense_variant|MODERATE|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.463A>G|p.Ile155Val|636/2068|463/1227|155/408||,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*3976A>G|||||3530|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*3976A>G|||||3548|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*3976A>G|||||3548|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*60677A>G|||||3600|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000456188|nonsense_mediated_decay||c.*42634A>G|||||3920|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*3600A>G|||||3600|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*3598A>G|||||3598| GT:AD:AF:DP 0/1:303,46:0.112:349 0/0:160,9:0.055:169 | |
| chr2 114257354 . A G . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=447;ECNT=2;FS=9.231;HCNT=7;MAX_ED=58;MIN_ED=58;MQ=56.26;MQ0=5;MQRankSum=-4.645;NLOD=26.42;ReadPosRankSum=-4.046;TLOD=6.12;ANN=G|missense_variant|MODERATE|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.521A>G|p.His174Arg|694/2068|521/1227|174/408||,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*4034A>G|||||3588|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*4034A>G|||||3606|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*4034A>G|||||3606|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*60735A>G|||||3658|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000456188|nonsense_mediated_decay||c.*42692A>G|||||3978|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*3658A>G|||||3658|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*3656A>G|||||3656| GT:AD:AF:DP 0/1:285,6:0.028:291 0/0:136,2:0.018:138 | |
| chr2 114257590 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=182;ECNT=2;FS=1.726;HCNT=16;MAX_ED=5;MIN_ED=5;MQ=54.07;MQ0=5;MQRankSum=-2.265;NLOD=14.46;ReadPosRankSum=-1.045;TLOD=7.76;ANN=C|missense_variant|MODERATE|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.757G>C|p.Ala253Pro|930/2068|757/1227|253/408||,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*4270G>C|||||3824|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*4270G>C|||||3842|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*4270G>C|||||3842|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*60971G>C|||||3894|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000456188|nonsense_mediated_decay||c.*42928G>C|||||4214|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*3894G>C|||||3894|,C|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*3892G>C|||||3892| GT:AD:AF:DP:PGT:PID 0/1:96,4:0.033:100:0|1:114257590_G_C 0/0:67,2:0.016:69:0|1:114257590_G_C | |
| chr2 114257595 . C G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=189;ECNT=2;FS=1.705;HCNT=16;MAX_ED=5;MIN_ED=5;MQ=54.27;MQ0=5;MQRankSum=-2.238;NLOD=14.46;ReadPosRankSum=-0.359;TLOD=7.73;ANN=G|synonymous_variant|LOW|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.762C>G|p.Pro254Pro|935/2068|762/1227|254/408||,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*4275C>G|||||3829|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*4275C>G|||||3847|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*4275C>G|||||3847|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*60976C>G|||||3899|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000456188|nonsense_mediated_decay||c.*42933C>G|||||4219|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*3899C>G|||||3899|,G|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*3897C>G|||||3897| GT:AD:AF:DP:PGT:PID 0/1:101,4:0.032:105:0|1:114257590_G_C 0/0:69,2:0.016:71:0|1:114257590_G_C | |
| chr2 114258536 . G A . t_lod_fstar ClippingRankSum=0;DP=256;ECNT=1;FS=1.931;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=50.96;MQ0=15;MQRankSum=0.263;NLOD=11.81;ReadPosRankSum=0.255;TLOD=4.49;ANN=A|3_prime_UTR_variant|MODIFIER|FOXD4L1|ENSG00000184492|transcript|ENST00000306507|protein_coding|1/1|c.*476G>A|||||476|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000259199|protein_coding||c.*5216G>A|||||4770|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000416503|protein_coding||c.*5216G>A|||||4788|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000433343|protein_coding||c.*5216G>A|||||4788|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000358604|nonsense_mediated_decay||c.*61917G>A|||||4840|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000479583|retained_intron||n.*4840G>A|||||4840|,A|downstream_gene_variant|MODIFIER|CBWD2|ENSG00000136682|transcript|ENST00000468417|retained_intron||n.*4838G>A|||||4838| GT:AD:AF:DP 0/1:127,6:0.051:133 0/0:85,13:0.143:98 | |
| chr2 114320751 . G A . PASS ClippingRankSum=0;DP=399;ECNT=1;FS=8.693;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=32.04;MQ0=89;MQRankSum=1.976;NLOD=3.22;ReadPosRankSum=3.896;TLOD=15.31;ANN=A|non_coding_transcript_exon_variant|MODIFIER|RP11-395L14.5|ENSG00000225398|transcript|ENST00000421970|processed_pseudogene|2/2|n.372G>A|||||| GT:AD:AF:DP 0/1:148,10:0.066:158 0/0:63,8:0.127:71 | |
| chr2 114335231 . C T . PASS ClippingRankSum=0;DP=806;ECNT=1;FS=9.246;HCNT=50;MAX_ED=.;MIN_ED=.;MQ=35.32;MQ0=212;MQRankSum=-1.763;NLOD=8.90;ReadPosRankSum=1.336;TLOD=29.27;ANN=T|non_coding_transcript_exon_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000432583|lincRNA|1/2|n.273C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000446648|lincRNA|1/3|n.273C>T|||||| GT:AD:AF:DP 0/1:309,24:0.089:333 0/0:205,19:0.085:224 | |
| chr2 114340615 . A C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1410;ECNT=2;FS=7.608;HCNT=4;MAX_ED=13;MIN_ED=13;MQ=53.65;MQ0=47;MQRankSum=-4.802;NLOD=59.64;ReadPosRankSum=-2.328;TLOD=29.97;ANN=C|upstream_gene_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene||n.-1049A>C|||||1049|,C|downstream_gene_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000432583|lincRNA||n.*4186A>C|||||4186|,C|downstream_gene_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000446648|lincRNA||n.*4186A>C|||||4186|,C|non_coding_transcript_exon_variant|MODIFIER|MIR1302-3|ENSG00000221055|transcript|ENST00000408128|miRNA|1/1|n.59T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:916,21:0.028:937:0|1:114340615_A_C 0/0:364,20:0.051:384:0|1:114340615_A_C | |
| chr2 114340628 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1374;ECNT=2;FS=2.342;HCNT=4;MAX_ED=13;MIN_ED=13;MQ=53.48;MQ0=56;MQRankSum=-3.655;NLOD=70.22;ReadPosRankSum=-2.274;TLOD=21.89;ANN=A|upstream_gene_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene||n.-1036C>A|||||1036|,A|downstream_gene_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000432583|lincRNA||n.*4199C>A|||||4199|,A|downstream_gene_variant|MODIFIER|FAM138B|ENSG00000226516|transcript|ENST00000446648|lincRNA||n.*4199C>A|||||4199|,A|non_coding_transcript_exon_variant|MODIFIER|MIR1302-3|ENSG00000221055|transcript|ENST00000408128|miRNA|1/1|n.46G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:895,13:0.02:908:0|1:114340615_A_C 0/0:360,15:0.044:375:0|1:114340615_A_C | |
| chr2 114350291 . G A . PASS ClippingRankSum=0;DP=1612;ECNT=1;FS=3.782;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=39.94;MQ0=656;MQRankSum=4.216;NLOD=50.23;ReadPosRankSum=-3.191;TLOD=14.84;ANN=A|upstream_gene_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron||n.-1462G>A|||||1462|,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|2/10|n.205-2349G>A||||||,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|1/9|n.155-2349G>A|||||| GT:AD:AF:DP 0/1:502,12:0.032:514 0/0:337,61:0.125:398 | |
| chr2 114351809 . AG A . PASS ClippingRankSum=0;DP=341;ECNT=1;FS=4.146;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=50.16;MQ0=29;MQRankSum=-1.013;NLOD=14.58;ReadPosRankSum=2.759;TLOD=8.54;ANN=A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*4796delC|||||4796|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*4803delC|||||4803|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*4803delC|||||4803|,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|2/10|n.205-827delG||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|1/9|n.155-827delG||||||INFO_REALIGN_3_PRIME,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|1/7|n.61delG||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:159,10:0.041:169 0/0:100,14:0.091:114 | |
| chr2 114353247 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=994;ECNT=4;FS=1.854;HCNT=6;MAX_ED=43;MIN_ED=12;MQ=45.08;MQ0=49;MQRankSum=-2.404;NLOD=41.92;ReadPosRankSum=-4.13;TLOD=14.33;ANN=T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*3359G>A|||||3359|,T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*3366G>A|||||3366|,T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*3366G>A|||||3366|,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|2/6|n.1134-23C>T||||||,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|4/10|n.451-23C>T||||||,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|3/9|n.401-23C>T|||||| GT:AD:AF:DP 0/1:573,21:0.027:594 0/0:277,6:0.025:283 | |
| chr2 114353259 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1073;ECNT=4;FS=0;HCNT=2;MAX_ED=43;MIN_ED=12;MQ=44.73;MQ0=53;MQRankSum=0.52;NLOD=50.25;ReadPosRankSum=-1.515;TLOD=14.14;ANN=A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*3347C>T|||||3347|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*3354C>T|||||3354|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*3354C>T|||||3354|,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|2/6|n.1134-11G>A||||||,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|4/10|n.451-11G>A||||||,A|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|3/9|n.401-11G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:632,11:0.016:643:0|1:114353259_G_A 0/0:285,14:0.038:299:0|1:114353259_G_A | |
| chr2 114353284 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1164;ECNT=4;FS=0;HCNT=2;MAX_ED=43;MIN_ED=12;MQ=44.86;MQ0=61;MQRankSum=0.314;NLOD=51.15;ReadPosRankSum=1.13;TLOD=11.48;ANN=A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*3322G>T|||||3322|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*3329G>T|||||3329|,A|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*3329G>T|||||3329|,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|3/7|n.1148C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|5/11|n.465C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|4/10|n.415C>A|||||| GT:AD:AF:DP:PGT:PID 0/1:680,12:0.014:692:0|1:114353259_G_A 0/0:314,14:0.038:328:0|1:114353259_G_A | |
| chr2 114353290 . T C . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1157;ECNT=4;FS=1.814;HCNT=7;MAX_ED=43;MIN_ED=12;MQ=44.88;MQ0=61;MQRankSum=-4.888;NLOD=2.03;ReadPosRankSum=3.988;TLOD=83.16;ANN=C|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*3316A>G|||||3316|,C|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*3323A>G|||||3323|,C|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*3323A>G|||||3323|,C|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|3/7|n.1154T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|5/11|n.471T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|4/10|n.421T>C|||||| GT:AD:AF:DP 0/1:602,89:0.122:691 0/0:293,33:0.09:326 | |
| chr2 114355054 . C T . PASS ClippingRankSum=0;DP=355;ECNT=1;FS=9.051;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=43.14;MQ0=32;MQRankSum=-0.657;NLOD=14.43;ReadPosRankSum=0.369;TLOD=21.96;ANN=T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000535848|unprocessed_pseudogene||n.*1552G>A|||||1552|,T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000437401|unprocessed_pseudogene||n.*1559G>A|||||1559|,T|downstream_gene_variant|MODIFIER|DDX11L2|ENSG00000236397|transcript|ENST00000457993|unprocessed_pseudogene||n.*1559G>A|||||1559|,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000538033|retained_intron|5/6|n.2002-9C>T||||||,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000326632|transcribed_unprocessed_pseudogene|8/10|n.1085-9C>T||||||,T|intron_variant|MODIFIER|WASH2P|ENSG00000146556|transcript|ENST00000453662|transcribed_unprocessed_pseudogene|7/9|n.1035-9C>T|||||| GT:AD:AF:DP 0/1:197,13:0.085:210 0/0:80,10:0.086:90 | |
| chr2 114369710 . C T . t_lod_fstar ClippingRankSum=0;DP=403;ECNT=1;FS=13.851;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=47.73;MQ0=53;MQRankSum=-3.398;NLOD=21.92;ReadPosRankSum=-1.672;TLOD=4.54;ANN=T|non_coding_transcript_exon_variant|MODIFIER|RPL23AP7|ENSG00000240356|transcript|ENST00000416673|processed_transcript|3/3|n.447G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RPL23AP7|ENSG00000240356|transcript|ENST00000391616|processed_transcript|3/3|n.289G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|RPL23AP7|ENSG00000240356|transcript|ENST00000449021|transcribed_processed_pseudogene|1/1|n.115G>A|||||| GT:AD:AF:DP 0/1:197,5:0.036:202 0/0:119,1:0.013:120 | |
| chr2 120438937 . G T . t_lod_fstar ClippingRankSum=0;DP=35;ECNT=1;FS=3.136;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=1.119;TLOD=4.18;ANN=T|missense_variant|MODERATE|TMEM177|ENSG00000144120|transcript|ENST00000272521|protein_coding|2/2|c.508G>T|p.Ala170Ser|637/1394|508/936|170/311||,T|missense_variant|MODERATE|TMEM177|ENSG00000144120|transcript|ENST00000401466|protein_coding|2/2|c.508G>T|p.Ala170Ser|589/1346|508/936|170/311||,T|missense_variant|MODERATE|TMEM177|ENSG00000144120|transcript|ENST00000424086|protein_coding|2/2|c.508G>T|p.Ala170Ser|981/1738|508/936|170/311||,T|downstream_gene_variant|MODIFIER|TMEM177|ENSG00000144120|transcript|ENST00000445518|protein_coding||c.*166G>T|||||166|WARNING_TRANSCRIPT_NO_STOP_CODON,T|intron_variant|MODIFIER|TMEM177|ENSG00000144120|transcript|ENST00000496203|processed_transcript|1/1|n.74+2085G>T||||||,T|intron_variant|MODIFIER|TMEM177|ENSG00000144120|transcript|ENST00000409951|protein_coding|2/2|c.270+238G>T|||||| GT:AD:AF:DP 0/1:17,2:0.118:19 0/0:16,0:0:16 | |
| chr2 128066306 . C T . PASS ClippingRankSum=0;DP=100;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.72;ReadPosRankSum=-1.933;TLOD=50.91;ANN=T|missense_variant|MODERATE|MAP3K2|ENSG00000169967|transcript|ENST00000344908|protein_coding|15/16|c.1489G>A|p.Val497Ile|1589/2135|1489/1860|497/619||,T|missense_variant|MODERATE|MAP3K2|ENSG00000169967|transcript|ENST00000409947|protein_coding|16/17|c.1489G>A|p.Val497Ile|1772/10992|1489/1860|497/619|| GT:AD:AF:DP 0/1:38,25:0.396:63 0/0:36,0:0:36 | |
| chr2 128363530 . G GT . germline_risk;t_lod_fstar DP=77;ECNT=1;FS=0;HCNT=37;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;NLOD=0.855;TLOD=5.29;ANN=GT|upstream_gene_variant|MODIFIER|MYO7B|ENSG00000169994|transcript|ENST00000563538|protein_coding||c.-3900_-3899insT|||||3898|WARNING_TRANSCRIPT_INCOMPLETE,GT|intron_variant|MODIFIER|MYO7B|ENSG00000169994|transcript|ENST00000389524|protein_coding|20/46|c.2424+27_2424+28insT||||||,GT|intron_variant|MODIFIER|MYO7B|ENSG00000169994|transcript|ENST00000428314|protein_coding|20/46|c.2424+27_2424+28insT||||||,GT|intron_variant|MODIFIER|MYO7B|ENSG00000169994|transcript|ENST00000409816|protein_coding|19/45|c.2424+27_2424+28insT|||||| GT:AD:AF:DP 0/1:0,6:1:6 0/0:0,0:nan:0 | |
| chr2 129026249 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=181;ECNT=4;FS=2.417;HCNT=30;MAX_ED=172;MIN_ED=96;MQ=44.24;MQ0=45;MQRankSum=-3.976;NLOD=5.75;ReadPosRankSum=1.54;TLOD=13.45;ANN=A|synonymous_variant|LOW|HS6ST1|ENSG00000136720|transcript|ENST00000259241|protein_coding|2/2|c.723C>T|p.Cys241Cys|737/3932|723/1236|241/411||,A|downstream_gene_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000463963|processed_transcript||n.*15C>T|||||15|,A|intron_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000469019|processed_transcript|1/2|n.361-22150C>T|||||| GT:AD:AF:DP 0/1:65,11:0.143:76 0/0:52,3:0.056:55 | |
| chr2 129026345 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=120;ECNT=4;FS=16.234;HCNT=32;MAX_ED=172;MIN_ED=96;MQ=51.96;MQ0=20;MQRankSum=-6.441;NLOD=2.64;ReadPosRankSum=0.799;TLOD=22.53;ANN=G|synonymous_variant|LOW|HS6ST1|ENSG00000136720|transcript|ENST00000259241|protein_coding|2/2|c.627T>C|p.His209His|641/3932|627/1236|209/411||,G|intron_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000469019|processed_transcript|1/2|n.361-22246T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000463963|processed_transcript|2/2|n.503T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:60,7:0.132:67:0|1:129026345_A_G 0/0:24,2:0.095:26:0|1:129026345_A_G | |
| chr2 129026358 . T C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=116;ECNT=4;FS=20.759;HCNT=32;MAX_ED=172;MIN_ED=96;MQ=52.3;MQ0=19;MQRankSum=-7.453;NLOD=4.21;ReadPosRankSum=1.192;TLOD=22.58;ANN=C|missense_variant|MODERATE|HS6ST1|ENSG00000136720|transcript|ENST00000259241|protein_coding|2/2|c.614A>G|p.Lys205Arg|628/3932|614/1236|205/411||,C|intron_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000469019|processed_transcript|1/2|n.361-22259A>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000463963|processed_transcript|2/2|n.490A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:64,7:0.135:71:0|1:129026345_A_G 0/0:19,1:0.067:20:0|1:129026345_A_G | |
| chr2 129026421 . A G . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=73;ECNT=4;FS=8.875;HCNT=35;MAX_ED=172;MIN_ED=96;MQ=57.41;MQ0=1;MQRankSum=-8.275;NLOD=3.01;ReadPosRankSum=-2.139;TLOD=7.11;ANN=G|missense_variant|MODERATE|HS6ST1|ENSG00000136720|transcript|ENST00000259241|protein_coding|2/2|c.551T>C|p.Leu184Pro|565/3932|551/1236|184/411||,G|intron_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000469019|processed_transcript|1/2|n.361-22322T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|HS6ST1|ENSG00000136720|transcript|ENST00000463963|processed_transcript|2/2|n.427T>C|||||| GT:AD:AF:DP 0/1:49,4:0.103:53 0/0:17,0:0:17 | |
| chr2 130872871 . C T . PASS ClippingRankSum=0;DP=728;ECNT=1;FS=1.237;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=46.76;MQ0=56;MQRankSum=-1.537;NLOD=17.79;ReadPosRankSum=7.274;TLOD=16.66;ANN=T|synonymous_variant|LOW|POTEF|ENSG00000196604|transcript|ENST00000357462|protein_coding|2/15|c.552G>A|p.Gly184Gly|646/4031|552/3228|184/1075||,T|synonymous_variant|LOW|POTEF|ENSG00000196604|transcript|ENST00000409914|protein_coding|4/17|c.552G>A|p.Gly184Gly|952/3842|552/3228|184/1075||,T|synonymous_variant|LOW|POTEF|ENSG00000196604|transcript|ENST00000360967|protein_coding|2/13|c.552G>A|p.Gly184Gly|604/2072|552/1131|184/376||,T|synonymous_variant|LOW|POTEF|ENSG00000196604|transcript|ENST00000361163|protein_coding|2/14|c.552G>A|p.Gly184Gly|604/2147|552/1185|184/394|| GT:AD:AF:DP 0/1:396,22:0.038:418 0/0:218,15:0.048:233 | |
| chr2 130897620 . A G . PASS ClippingRankSum=0;DP=32;ECNT=1;FS=3.905;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=54.91;MQ0=1;MQRankSum=-4.583;NLOD=2.62;ReadPosRankSum=-0.822;TLOD=16.13;ANN=G|missense_variant|MODERATE|CCDC74B|ENSG00000152076|transcript|ENST00000392984|protein_coding|5/7|c.1232T>C|p.Val411Ala|1976/2459|1232/1449|411/482||,G|missense_variant|MODERATE|CCDC74B|ENSG00000152076|transcript|ENST00000409943|protein_coding|6/8|c.728T>C|p.Val243Ala|811/1296|728/945|243/314||,G|missense_variant|MODERATE|CCDC74B|ENSG00000152076|transcript|ENST00000310463|protein_coding|6/8|c.926T>C|p.Val309Ala|1064/1549|926/1143|309/380||,G|downstream_gene_variant|MODIFIER|MED15P9|ENSG00000223760|transcript|ENST00000427638|processed_transcript||n.*630A>G|||||630|,G|downstream_gene_variant|MODIFIER|MED15P9|ENSG00000223760|transcript|ENST00000424716|transcribed_unprocessed_pseudogene||n.*2288A>G|||||2288|,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000423263|nonsense_mediated_decay||c.*2254T>C|||||236|,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000409128|protein_coding||c.*1107T>C|||||970|,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000434929|nonsense_mediated_decay||c.*4396T>C|||||1111|,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000457413|protein_coding||c.*2141T>C|||||2141|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000409234|protein_coding||c.*2839T>C|||||2733|,G|downstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000441670|protein_coding||c.*3164T>C|||||3164|WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000496704|retained_intron|2/4|n.2900T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000498526|retained_intron|1/2|n.27T>C|||||| GT:AD:AF:DP 0/1:10,8:0.412:18 0/0:12,0:0:12 | |
| chr2 130900789 . C A . t_lod_fstar ClippingRankSum=0;DP=97;ECNT=1;FS=0;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.62;ReadPosRankSum=0.875;TLOD=4.41;ANN=A|missense_variant|MODERATE|CCDC74B|ENSG00000152076|transcript|ENST00000409234|protein_coding|2/2|c.348G>T|p.Glu116Asp|435/871|348/678|116/225||,A|missense_variant|MODERATE|CCDC74B|ENSG00000152076|transcript|ENST00000441670|protein_coding|2/2|c.474G>T|p.Glu158Asp|556/561|474/479|158/158||WARNING_TRANSCRIPT_INCOMPLETE,A|5_prime_UTR_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000392984|protein_coding|2/7|c.-234G>T|||||234|,A|upstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000496704|retained_intron||n.-188G>T|||||188|,A|upstream_gene_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000498526|retained_intron||n.-3143G>T|||||3143|,A|downstream_gene_variant|MODIFIER|MED15P9|ENSG00000223760|transcript|ENST00000427638|processed_transcript||n.*3799C>A|||||3799|,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000409943|protein_coding|2/7|c.295+53G>T||||||,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000310463|protein_coding|2/7|c.295+53G>T||||||,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000423263|nonsense_mediated_decay|2/4|c.295+53G>T||||||,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000409128|protein_coding|2/3|c.421+53G>T||||||,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000434929|nonsense_mediated_decay|3/4|c.*116+53G>T||||||,A|intron_variant|MODIFIER|CCDC74B|ENSG00000152076|transcript|ENST00000457413|protein_coding|2/2|c.418+53G>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:70,1:0.043:71 0/0:26,0:0:26 | |
| chr2 130912720 . G A . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=198;ECNT=3;FS=3.917;HCNT=31;MAX_ED=69;MIN_ED=58;MQ=56.9;MQ0=5;MQRankSum=-13.584;NLOD=8.42;ReadPosRankSum=2.992;TLOD=14.51;ANN=A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000409031|protein_coding|15/20|c.1519C>T|p.Arg507*|2668/4896|1519/2601|507/866||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000351288|protein_coding|14/19|c.1432C>T|p.Arg478*|1432/3661|1432/2514|478/837||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000439886|protein_coding|10/15|c.1141C>T|p.Arg381*|1143/3371|1141/2223|381/740||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000453750|protein_coding|8/13|c.766C>T|p.Arg256*|766/2994|766/1848|256/615||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000431183|protein_coding|12/17|c.1213C>T|p.Arg405*|2362/4590|1213/2295|405/764||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000443958|protein_coding|8/13|c.511C>T|p.Arg171*|807/2350|511/1593|171/530||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000339679|protein_coding|13/18|c.1093C>T|p.Arg365*|1348/2723|1093/2175|365/724||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000452225|protein_coding|10/15|c.742C>T|p.Arg248*|981/2342|742/1824|248/607||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000426662|protein_coding|7/12|c.427C>T|p.Arg143*|660/1861|427/1509|143/502||,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000457039|protein_coding|4/7|c.310C>T|p.Arg104*|310/940|310/940|104/312||WARNING_TRANSCRIPT_INCOMPLETE,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000449159|protein_coding|2/5|c.127C>T|p.Arg43*|127/635|127/635|43/210||WARNING_TRANSCRIPT_INCOMPLETE,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000430682|protein_coding|5/6|c.562C>T|p.Arg188*|563/820|562/819|188/272||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|SMPD4|ENSG00000136699|transcript|ENST00000451542|protein_coding|7/7|c.745C>T|p.Arg249*|745/796|745/796|249/264||WARNING_TRANSCRIPT_INCOMPLETE,A|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000454468|nonsense_mediated_decay|14/19|c.*1106C>T|||||18181|,A|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000412570|nonsense_mediated_decay|14/19|c.*1089C>T|||||18410|,A|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000433118|nonsense_mediated_decay|11/16|c.*820C>T|||||12399|,A|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000435455|nonsense_mediated_decay|8/8|c.*195C>T|||||970|,A|upstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491319|retained_intron||n.-1047C>T|||||1047|,A|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000473720|processed_transcript||n.*880C>T|||||880|,A|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000455548|processed_transcript||n.*899C>T|||||899|,A|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000439029|nonsense_mediated_decay||c.*12399C>T|||||2214|,A|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491128|retained_intron|2/7|n.342C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000482171|retained_intron|3/7|n.1457C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000461187|retained_intron|2/3|n.219C>T||||||;LOF=(SMPD4|ENSG00000136699|25|0.48);NMD=(SMPD4|ENSG00000136699|25|0.48) GT:AD:AF:DP 0/1:135,14:0.095:149 0/0:37,0:0:37 | |
| chr2 130912778 . A G . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=171;ECNT=3;FS=1.079;HCNT=39;MAX_ED=69;MIN_ED=58;MQ=57.67;MQ0=1;MQRankSum=-12.825;NLOD=8.13;ReadPosRankSum=-1.729;TLOD=28.04;ANN=G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000409031|protein_coding|15/20|c.1461T>C|p.Phe487Phe|2610/4896|1461/2601|487/866||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000351288|protein_coding|14/19|c.1374T>C|p.Phe458Phe|1374/3661|1374/2514|458/837||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000439886|protein_coding|10/15|c.1083T>C|p.Phe361Phe|1085/3371|1083/2223|361/740||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000453750|protein_coding|8/13|c.708T>C|p.Phe236Phe|708/2994|708/1848|236/615||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000431183|protein_coding|12/17|c.1155T>C|p.Phe385Phe|2304/4590|1155/2295|385/764||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000443958|protein_coding|8/13|c.453T>C|p.Phe151Phe|749/2350|453/1593|151/530||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000339679|protein_coding|13/18|c.1035T>C|p.Phe345Phe|1290/2723|1035/2175|345/724||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000452225|protein_coding|10/15|c.684T>C|p.Phe228Phe|923/2342|684/1824|228/607||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000426662|protein_coding|7/12|c.369T>C|p.Phe123Phe|602/1861|369/1509|123/502||,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000457039|protein_coding|4/7|c.252T>C|p.Phe84Phe|252/940|252/940|84/312||WARNING_TRANSCRIPT_INCOMPLETE,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000449159|protein_coding|2/5|c.69T>C|p.Phe23Phe|69/635|69/635|23/210||WARNING_TRANSCRIPT_INCOMPLETE,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000430682|protein_coding|5/6|c.504T>C|p.Phe168Phe|505/820|504/819|168/272||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|SMPD4|ENSG00000136699|transcript|ENST00000451542|protein_coding|7/7|c.687T>C|p.Phe229Phe|687/796|687/796|229/264||WARNING_TRANSCRIPT_INCOMPLETE,G|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000454468|nonsense_mediated_decay|14/19|c.*1048T>C|||||18123|,G|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000412570|nonsense_mediated_decay|14/19|c.*1031T>C|||||18352|,G|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000433118|nonsense_mediated_decay|11/16|c.*762T>C|||||12341|,G|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000435455|nonsense_mediated_decay|8/8|c.*137T>C|||||912|,G|upstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491319|retained_intron||n.-1105T>C|||||1105|,G|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000473720|processed_transcript||n.*822T>C|||||822|,G|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000455548|processed_transcript||n.*841T>C|||||841|,G|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000439029|nonsense_mediated_decay||c.*12341T>C|||||2156|,G|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491128|retained_intron|2/7|n.284T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000482171|retained_intron|3/7|n.1399T>C||||||,G|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000461187|retained_intron|2/3|n.161T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:114,14:0.106:128:0|1:130912778_A_G 0/0:38,0:0:38:0|1:130912778_A_G | |
| chr2 130912789 . A C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=156;ECNT=3;FS=1.063;HCNT=39;MAX_ED=69;MIN_ED=58;MQ=57.63;MQ0=1;MQRankSum=-12.266;NLOD=7.22;ReadPosRankSum=-3.441;TLOD=27.98;ANN=C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000409031|protein_coding|15/20|c.1450T>G|p.Phe484Val|2599/4896|1450/2601|484/866||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000351288|protein_coding|14/19|c.1363T>G|p.Phe455Val|1363/3661|1363/2514|455/837||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000439886|protein_coding|10/15|c.1072T>G|p.Phe358Val|1074/3371|1072/2223|358/740||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000453750|protein_coding|8/13|c.697T>G|p.Phe233Val|697/2994|697/1848|233/615||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000431183|protein_coding|12/17|c.1144T>G|p.Phe382Val|2293/4590|1144/2295|382/764||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000443958|protein_coding|8/13|c.442T>G|p.Phe148Val|738/2350|442/1593|148/530||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000339679|protein_coding|13/18|c.1024T>G|p.Phe342Val|1279/2723|1024/2175|342/724||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000452225|protein_coding|10/15|c.673T>G|p.Phe225Val|912/2342|673/1824|225/607||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000426662|protein_coding|7/12|c.358T>G|p.Phe120Val|591/1861|358/1509|120/502||,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000457039|protein_coding|4/7|c.241T>G|p.Phe81Val|241/940|241/940|81/312||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000449159|protein_coding|2/5|c.58T>G|p.Phe20Val|58/635|58/635|20/210||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000430682|protein_coding|5/6|c.493T>G|p.Phe165Val|494/820|493/819|165/272||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|SMPD4|ENSG00000136699|transcript|ENST00000451542|protein_coding|7/7|c.676T>G|p.Phe226Val|676/796|676/796|226/264||WARNING_TRANSCRIPT_INCOMPLETE,C|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000454468|nonsense_mediated_decay|14/19|c.*1037T>G|||||18112|,C|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000412570|nonsense_mediated_decay|14/19|c.*1020T>G|||||18341|,C|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000433118|nonsense_mediated_decay|11/16|c.*751T>G|||||12330|,C|3_prime_UTR_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000435455|nonsense_mediated_decay|8/8|c.*126T>G|||||901|,C|upstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491319|retained_intron||n.-1116T>G|||||1116|,C|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000473720|processed_transcript||n.*811T>G|||||811|,C|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000455548|processed_transcript||n.*830T>G|||||830|,C|downstream_gene_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000439029|nonsense_mediated_decay||c.*12330T>G|||||2145|,C|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000491128|retained_intron|2/7|n.273T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000482171|retained_intron|3/7|n.1388T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|SMPD4|ENSG00000136699|transcript|ENST00000461187|retained_intron|2/3|n.150T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:102,14:0.105:116:0|1:130912778_A_G 0/0:36,0:0:36:0|1:130912778_A_G | |
| chr2 130952609 . C G . t_lod_fstar ClippingRankSum=0;DP=130;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=52;MQ0=3;MQRankSum=-1.372;NLOD=7.22;ReadPosRankSum=0.694;TLOD=4.25;ANN=G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000409255|protein_coding||c.*4410C>G|||||4324|,G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000425361|protein_coding||c.*4410C>G|||||4323|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000457492|protein_coding||c.*4410C>G|||||4341|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000281871|protein_coding||c.*4410C>G|||||4309|,G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000455239|protein_coding||c.*4345C>G|||||4307|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MZT2B|ENSG00000152082|transcript|ENST00000480182|retained_intron||n.*4309C>G|||||4309|,G|intron_variant|MODIFIER|TUBA3E|ENSG00000152086|transcript|ENST00000312988|protein_coding|3/4|c.375+43G>C|||||| GT:AD:AF:DP 0/1:92,1:0.029:93 0/0:33,0:0:33 | |
| chr2 131175817 . G T . t_lod_fstar ClippingRankSum=0;DP=619;ECNT=1;FS=1.517;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=44.52;MQ0=229;MQRankSum=0.169;NLOD=20.62;ReadPosRankSum=-2.494;TLOD=5.49;ANN=T|downstream_gene_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000413041|transcribed_unprocessed_pseudogene||n.*827C>A|||||827|,T|downstream_gene_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000438056|processed_transcript||n.*915C>A|||||915|,T|intron_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000449066|processed_transcript|2/2|n.223+827C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000430785|retained_intron|2/2|n.3176C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000424873|processed_transcript|4/4|n.581C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000423905|processed_transcript|5/5|n.462C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|FAR2P2|ENSG00000178162|transcript|ENST00000433703|processed_transcript|6/6|n.593C>A|||||| GT:AD:AF:DP 0/1:172,6:0.027:178 0/0:205,1:0.006757:206 | |
| chr2 131377636 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=1184;ECNT=2;FS=17.814;HCNT=16;MAX_ED=32;MIN_ED=32;MQ=45.92;MQ0=119;MQRankSum=-4.17;NLOD=15.67;ReadPosRankSum=-1.633;TLOD=43.33;ANN=T|synonymous_variant|LOW|POTEJ|ENSG00000222038|transcript|ENST00000409602|protein_coding|4/15|c.718C>T|p.Leu240Leu|770/3383|718/3117|240/1038||,T|upstream_gene_variant|MODIFIER|RNU6-848P|ENSG00000251757|transcript|ENST00000515948|snRNA||n.-2775C>T|||||2775| GT:AD:AF:DP 0/1:510,31:0.076:541 0/0:360,22:0.075:382 | |
| chr2 131377668 . G C . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=831;ECNT=2;FS=4.684;HCNT=19;MAX_ED=32;MIN_ED=32;MQ=44.32;MQ0=134;MQRankSum=-3.138;NLOD=35.07;ReadPosRankSum=0.726;TLOD=10.58;ANN=C|synonymous_variant|LOW|POTEJ|ENSG00000222038|transcript|ENST00000409602|protein_coding|4/15|c.750G>C|p.Val250Val|802/3383|750/3117|250/1038||,C|upstream_gene_variant|MODIFIER|RNU6-848P|ENSG00000251757|transcript|ENST00000515948|snRNA||n.-2743G>C|||||2743| GT:AD:AF:DP 0/1:307,12:0.045:319 0/0:275,8:0.037:283 | |
| chr2 131412635 . C A . t_lod_fstar ClippingRankSum=0;DP=1275;ECNT=1;FS=0.765;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=34.66;MQ0=762;MQRankSum=3.085;NLOD=12.05;ReadPosRankSum=0.13;TLOD=4.81;ANN=A|upstream_gene_variant|MODIFIER|AC140481.1|ENSG00000257010|transcript|ENST00000535037|processed_pseudogene||n.-1937C>A|||||1937|,A|intron_variant|MODIFIER|POTEJ|ENSG00000222038|transcript|ENST00000409602|protein_coding|14/14|c.1788+21C>A|||||| GT:AD:AF:DP 0/1:89,4:0.055:93 0/0:339,69:0.168:408 | |
| chr2 131976353 . C T . PASS ClippingRankSum=0;DP=360;ECNT=1;FS=36.433;HCNT=20;MAX_ED=.;MIN_ED=.;MQ=52.38;MQ0=19;MQRankSum=-3.073;NLOD=5.07;ReadPosRankSum=1.353;TLOD=24.20;ANN=T|splice_region_variant&non_coding_transcript_exon_variant|LOW|AC131180.1|ENSG00000250852|transcript|ENST00000514256|unprocessed_pseudogene|2/15|n.58C>T||||||,T|synonymous_variant|LOW|POTEE|ENSG00000188219|transcript|ENST00000356920|protein_coding|1/15|c.378C>T|p.Ser126Ser|472/4031|378/3228|126/1075||,T|synonymous_variant|LOW|POTEE|ENSG00000188219|transcript|ENST00000358087|protein_coding|1/14|c.378C>T|p.Ser126Ser|430/3399|378/1185|126/394||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.423+85789C>T||||||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.423+85789C>T|||||| GT:AD:AF:DP 0/1:211,13:0.08:224 0/0:95,10:0.12:105 | |
| chr2 131995700 . C T . t_lod_fstar ClippingRankSum=0;DP=1297;ECNT=1;FS=0;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=51.7;MQ0=55;MQRankSum=2.637;NLOD=46.21;ReadPosRankSum=0.488;TLOD=6.21;ANN=T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.423+105136C>T||||||,T|intron_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000356920|protein_coding|7/14|c.1198-67C>T||||||,T|intron_variant|MODIFIER|AC131180.1|ENSG00000250852|transcript|ENST00000514256|unprocessed_pseudogene|8/14|n.876-67C>T||||||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.423+105136C>T||||||,T|intron_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000358087|protein_coding|6/13|c.1157-67C>T|||||| GT:AD:AF:DP 0/1:818,9:0.016:827 0/0:378,31:0.085:409 | |
| chr2 132010541 . T C . PASS ClippingRankSum=0;DP=1081;ECNT=1;FS=19.787;HCNT=21;MAX_ED=.;MIN_ED=.;MQ=44.64;MQ0=53;MQRankSum=-1.7;NLOD=40.39;ReadPosRankSum=-4.71;TLOD=18.36;ANN=C|synonymous_variant|LOW|POTEE|ENSG00000188219|transcript|ENST00000356920|protein_coding|13/15|c.1647T>C|p.His549His|1741/4031|1647/3228|549/1075||,C|3_prime_UTR_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000358087|protein_coding|12/14|c.*421T>C|||||14746|,C|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-100052T>C||||||,C|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-100052T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC131180.1|ENSG00000250852|transcript|ENST00000514256|unprocessed_pseudogene|13/15|n.1261T>C|||||| GT:AD:AF:DP 0/1:668,19:0.042:687 0/0:289,14:0.056:303 | |
| chr2 132044701 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=294;ECNT=5;FS=7.074;HCNT=6;MAX_ED=12;MIN_ED=6;MQ=44.07;MQ0=68;MQRankSum=1.331;NLOD=3.06;ReadPosRankSum=-4.564;TLOD=14.35;ANN=A|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.20G>A|p.Cys7Tyr|372/2249|20/357|7/118||,A|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1625G>A|||||1625|,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65892G>A||||||,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65892G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:109,7:0.062:116:0|1:132044701_G_A 0/0:87,4:0.044:91:0|1:132044701_G_A | |
| chr2 132044707 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=297;ECNT=5;FS=6.696;HCNT=6;MAX_ED=12;MIN_ED=6;MQ=44.92;MQ0=63;MQRankSum=1.23;NLOD=3.36;ReadPosRankSum=-4.108;TLOD=14.35;ANN=A|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.26G>A|p.Gly9Asp|378/2249|26/357|9/118||,A|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1619G>A|||||1619|,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65886G>A||||||,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65886G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:116,7:0.062:123:0|1:132044701_G_A 0/0:87,4:0.043:91:0|1:132044701_G_A | |
| chr2 132044708 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=297;ECNT=5;FS=6.696;HCNT=6;MAX_ED=12;MIN_ED=6;MQ=44.92;MQ0=63;MQRankSum=1.23;NLOD=3.36;ReadPosRankSum=-4.102;TLOD=14.30;ANN=A|synonymous_variant|LOW|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.27T>A|p.Gly9Gly|379/2249|27/357|9/118||,A|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1618T>A|||||1618|,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65885T>A||||||,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65885T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:116,7:0.06:123:0|1:132044701_G_A 0/0:87,4:0.043:91:0|1:132044701_G_A | |
| chr2 132044712 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=303;ECNT=5;FS=4.702;HCNT=6;MAX_ED=12;MIN_ED=6;MQ=45.3;MQ0=62;MQRankSum=1.171;NLOD=3.06;ReadPosRankSum=-3.723;TLOD=14.22;ANN=G|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.31A>G|p.Arg11Gly|383/2249|31/357|11/118||,G|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1614A>G|||||1614|,G|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65881A>G||||||,G|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65881A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:121,7:0.058:128:0|1:132044701_G_A 0/0:88,4:0.044:92:0|1:132044701_G_A | |
| chr2 132044713 . G T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=307;ECNT=5;FS=4.703;HCNT=6;MAX_ED=12;MIN_ED=6;MQ=45.39;MQ0=63;MQRankSum=1.142;NLOD=3.06;ReadPosRankSum=-3.529;TLOD=14.24;ANN=T|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.32G>T|p.Arg11Ile|384/2249|32/357|11/118||,T|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1613G>T|||||1613|,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65880G>T||||||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65880G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:124,7:0.059:131:0|1:132044701_G_A 0/0:88,4:0.044:92:0|1:132044701_G_A | |
| chr2 132044849 . T A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=305;ECNT=6;FS=5.194;HCNT=17;MAX_ED=73;MIN_ED=54;MQ=54.58;MQ0=22;MQRankSum=-5.457;NLOD=5.29;ReadPosRankSum=3.544;TLOD=12.17;ANN=A|synonymous_variant|LOW|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.168T>A|p.Pro56Pro|520/2249|168/357|56/118||,A|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1477T>A|||||1477|,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65744T>A||||||,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65744T>A|||||| GT:AD:AF:DP 0/1:162,10:0.056:172 0/0:93,6:0.063:99 | |
| chr2 132044903 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=260;ECNT=6;FS=4.674;HCNT=20;MAX_ED=73;MIN_ED=54;MQ=51.79;MQ0=19;MQRankSum=-2.203;NLOD=4.26;ReadPosRankSum=-3.847;TLOD=13.59;ANN=A|synonymous_variant|LOW|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.222G>A|p.Leu74Leu|574/2249|222/357|74/118||,A|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1423G>A|||||1423|,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65690G>A||||||,A|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65690G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:140,7:0.044:147:0|1:132044903_G_A 0/0:83,3:0.047:86:0|1:132044903_G_A | |
| chr2 132044904 . GTACC G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=266;ECNT=6;FS=4.675;HCNT=20;MAX_ED=73;MIN_ED=54;MQ=51.6;MQ0=19;MQRankSum=-2.035;NLOD=4.86;ReadPosRankSum=-3.938;TLOD=13.55;ANN=G|frameshift_variant|HIGH|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.228_231delTACC|p.Thr77fs|580/2249|228/357|76/118||INFO_REALIGN_3_PRIME,G|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1421_-1418delTACC|||||1421|,G|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65684_424-65681delTACC||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65684_424-65681delTACC||||||INFO_REALIGN_3_PRIME;LOF=(CYP4F31P|ENSG00000178206|1|1.00) GT:AD:AF:DP:PGT:PID 0/1:144,7:0.043:151:0|1:132044903_G_A 0/0:85,3:0.045:88:0|1:132044903_G_A | |
| chr2 132044916 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=255;ECNT=6;FS=1.612;HCNT=20;MAX_ED=73;MIN_ED=54;MQ=51.14;MQ0=19;MQRankSum=-0.814;NLOD=8.46;ReadPosRankSum=-3.754;TLOD=7.51;ANN=T|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.235C>T|p.Pro79Ser|587/2249|235/357|79/118||,T|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1410C>T|||||1410|,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65677C>T||||||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65677C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:143,4:0.027:147:0|1:132044903_G_A 0/0:80,2:0.032:82:0|1:132044903_G_A | |
| chr2 132044919 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=256;ECNT=6;FS=4.18;HCNT=20;MAX_ED=73;MIN_ED=54;MQ=51.24;MQ0=18;MQRankSum=-1.083;NLOD=8.46;ReadPosRankSum=-3.512;TLOD=7.48;ANN=T|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.238C>T|p.Arg80Trp|590/2249|238/357|80/118||,T|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1407C>T|||||1407|,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65674C>T||||||,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65674C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:147,4:0.026:151:0|1:132044903_G_A 0/0:81,1:0.032:82:0|1:132044903_G_A | |
| chr2 132044922 . A C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=254;ECNT=6;FS=5.972;HCNT=20;MAX_ED=73;MIN_ED=54;MQ=51.42;MQ0=15;MQRankSum=-0.517;NLOD=12.96;ReadPosRankSum=-2.787;TLOD=4.65;ANN=C|missense_variant|MODERATE|CYP4F31P|ENSG00000178206|transcript|ENST00000416266|protein_coding|1/5|c.241A>C|p.Ile81Leu|593/2249|241/357|81/118||,C|upstream_gene_variant|MODIFIER|FAR2P4|ENSG00000231431|transcript|ENST00000560285|processed_transcript||n.-1404A>C|||||1404|,C|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000303908|protein_coding|5/5|c.424-65671A>C||||||,C|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460|protein_coding|6/6|c.424-65671A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:152,2:0.018:154:0|1:132044903_G_A 0/0:80,1:0.016:81:0|1:132044903_G_A | |
| chr2 132237732 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=134;ECNT=2;FS=13.482;HCNT=1;MAX_ED=18;MIN_ED=18;MQ=55.3;MQ0=4;MQRankSum=-4.274;NLOD=7.15;ReadPosRankSum=-1.575;TLOD=29.35;ANN=T|missense_variant|MODERATE|TUBA3D|ENSG00000075886|transcript|ENST00000321253|protein_coding|4/5|c.466C>T|p.Arg156Trp|573/1546|466/1353|156/450||,T|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000309451|protein_coding||c.*3902G>A|||||3801|,T|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000410036|processed_transcript||n.*3799G>A|||||3799|,T|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000427024|nonsense_mediated_decay|2/4|c.278-7977G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000445782|retained_intron|2/3|n.331-7977G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|TUBA3D|ENSG00000075886|transcript|ENST00000409047|processed_transcript|3/3|n.292C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:64,9:0.145:73:0|1:132237732_C_T 0/0:52,5:0.095:57:0|1:132237732_C_T | |
| chr2 132237750 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=129;ECNT=2;FS=17.602;HCNT=1;MAX_ED=18;MIN_ED=18;MQ=54.84;MQ0=3;MQRankSum=-4.564;NLOD=5.73;ReadPosRankSum=-0.254;TLOD=34.57;ANN=A|missense_variant|MODERATE|TUBA3D|ENSG00000075886|transcript|ENST00000321253|protein_coding|4/5|c.484G>A|p.Gly162Ser|591/1546|484/1353|162/450||,A|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000309451|protein_coding||c.*3884C>T|||||3783|,A|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000410036|processed_transcript||n.*3781C>T|||||3781|,A|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000427024|nonsense_mediated_decay|2/4|c.278-7995C>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000445782|retained_intron|2/3|n.331-7995C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|TUBA3D|ENSG00000075886|transcript|ENST00000409047|processed_transcript|3/3|n.310G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:66,11:0.177:77:0|1:132237732_C_T 0/0:44,5:0.108:49:0|1:132237732_C_T | |
| chr2 132237927 . C A . PASS ClippingRankSum=0;DP=197;ECNT=1;FS=21.412;HCNT=21;MAX_ED=.;MIN_ED=.;MQ=52.22;MQ0=6;MQRankSum=-5.082;NLOD=12.91;ReadPosRankSum=-3.247;TLOD=36.64;ANN=A|missense_variant|MODERATE|TUBA3D|ENSG00000075886|transcript|ENST00000321253|protein_coding|4/5|c.661C>A|p.Arg221Ser|768/1546|661/1353|221/450||,A|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000309451|protein_coding||c.*3707G>T|||||3606|,A|downstream_gene_variant|MODIFIER|TUBA3D|ENSG00000075886|transcript|ENST00000409047|processed_transcript||n.*16C>A|||||16|,A|downstream_gene_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000410036|processed_transcript||n.*3604G>T|||||3604|,A|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000427024|nonsense_mediated_decay|2/4|c.278-8172G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|MZT2A|ENSG00000173272|transcript|ENST00000445782|retained_intron|2/3|n.331-8172G>T|||||| GT:AD:AF:DP 0/1:92,17:0.198:109 0/0:76,2:0.018:78 | |
| chr2 132288362 . T C . t_lod_fstar ClippingRankSum=0;DP=113;ECNT=1;FS=9.378;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=54.46;MQ0=8;MQRankSum=-2.345;NLOD=2.33;ReadPosRankSum=0.604;TLOD=4.95;ANN=C|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000295171|protein_coding|3/8|c.506T>C|p.Met169Thr|644/1543|506/1137|169/378||,C|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000409856|protein_coding|3/8|c.308T>C|p.Met103Thr|399/1298|308/939|103/312||,C|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000434330|protein_coding|2/5|c.293T>C|p.Met98Thr|524/851|293/620|98/205||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000467992|protein_coding|1/5|c.812T>C|p.Met271Thr|1126/2809|812/993|271/330||,C|3_prime_UTR_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000454549|nonsense_mediated_decay|4/4|c.*359T>C|||||2265|,C|downstream_gene_variant|MODIFIER|MED15P4|ENSG00000224679|transcript|ENST00000417579|unprocessed_pseudogene||n.*4398A>G|||||4398|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000465939|retained_intron||n.*609T>C|||||609|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000468650|retained_intron||n.*1098T>C|||||1098|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000478665|processed_transcript||n.*1040T>C|||||1040| GT:AD:AF:DP 0/1:66,4:0.078:70 0/0:32,3:0.074:35 | |
| chr2 132290415 . T C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=72;ECNT=2;FS=14.645;HCNT=13;MAX_ED=26;MIN_ED=26;MQ=54.79;MQ0=2;MQRankSum=-2.468;NLOD=2.34;ReadPosRankSum=-2.072;TLOD=5.42;ANN=C|downstream_gene_variant|MODIFIER|MED15P4|ENSG00000224679|transcript|ENST00000417579|unprocessed_pseudogene||n.*2345A>G|||||2345|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000465939|retained_intron||n.*2662T>C|||||2662|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000454549|nonsense_mediated_decay||c.*4318T>C|||||2005|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000468650|retained_intron||n.*3151T>C|||||3151|,C|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000478665|processed_transcript||n.*3093T>C|||||3093|,C|intron_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000295171|protein_coding|5/7|c.877-22T>C||||||,C|intron_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000409856|protein_coding|5/7|c.679-22T>C||||||,C|intron_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000434330|protein_coding|4/4|c.543-22T>C||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000467992|protein_coding|2/4|c.*976-22T>C|||||| GT:AD:AF:DP 0/1:48,3:0.081:51 0/0:18,1:0.053:19 | |
| chr2 132290441 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=56;ECNT=2;FS=4.451;HCNT=34;MAX_ED=26;MIN_ED=26;MQ=58;MQ0=1;MQRankSum=-4.656;NLOD=2.44;ReadPosRankSum=-1.728;TLOD=5.76;ANN=A|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000295171|protein_coding|6/8|c.881G>A|p.Arg294Gln|1019/1543|881/1137|294/378||,A|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000409856|protein_coding|6/8|c.683G>A|p.Arg228Gln|774/1298|683/939|228/312||,A|missense_variant|MODERATE|CCDC74A|ENSG00000163040|transcript|ENST00000434330|protein_coding|5/5|c.547G>A|p.Gly183Ser|778/851|547/620|183/205||WARNING_TRANSCRIPT_INCOMPLETE,A|3_prime_UTR_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000467992|protein_coding|3/5|c.*980G>A|||||1062|,A|downstream_gene_variant|MODIFIER|MED15P4|ENSG00000224679|transcript|ENST00000417579|unprocessed_pseudogene||n.*2319C>T|||||2319|,A|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000465939|retained_intron||n.*2688G>A|||||2688|,A|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000454549|nonsense_mediated_decay||c.*4344G>A|||||2031|,A|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000468650|retained_intron||n.*3177G>A|||||3177|,A|downstream_gene_variant|MODIFIER|CCDC74A|ENSG00000163040|transcript|ENST00000478665|processed_transcript||n.*3119G>A|||||3119| GT:AD:AF:DP 0/1:30,4:0.097:34 0/0:20,1:0.05:21 | |
| chr2 132860367 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=282;ECNT=2;FS=0;HCNT=13;MAX_ED=20;MIN_ED=20;MQ=57.93;MQ0=14;MQRankSum=-4.961;NLOD=13.86;ReadPosRankSum=-0.237;TLOD=4.59;ANN=A|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*230G>A|||||230|,A|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132860367G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:171,3:0.017:174:0|1:132860367_G_A 0/0:86,2:0.016:88:0|1:132860367_G_A | |
| chr2 132860387 . T A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=242;ECNT=2;FS=0;HCNT=13;MAX_ED=20;MIN_ED=20;MQ=58.07;MQ0=12;MQRankSum=-4.584;NLOD=12.06;ReadPosRankSum=1.725;TLOD=4.67;ANN=A|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*250T>A|||||250|,A|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132860387T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:148,3:0.018:151:0|1:132860367_G_A 0/0:73,2:0.018:75:0|1:132860367_G_A | |
| chr2 132861220 . T TAA . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=289;ECNT=4;FS=0;HCNT=3;MAX_ED=153;MIN_ED=133;MQ=55.26;MQ0=22;MQRankSum=-2.785;NLOD=16.86;ReadPosRankSum=1.108;TLOD=4.59;ANN=TAA|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*1083_*1084insAA|||||1084|,TAA|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132861220_132861221insAA|||||| GT:AD:AF:DP 0/1:174,2:0.017:176 0/0:77,1:0.018:78 | |
| chr2 132861353 . G A . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=300;ECNT=4;FS=5.708;HCNT=8;MAX_ED=153;MIN_ED=133;MQ=55.68;MQ0=11;MQRankSum=-2.43;NLOD=12.96;ReadPosRankSum=0.5;TLOD=4.46;ANN=A|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*1216G>A|||||1216|,A|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132861353G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:192,2:0.014:194:0|1:132861353_G_A 0/0:84,1:0.017:85:0|1:132861353_G_A | |
| chr2 132861355 . A C . clustered_events;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=302;ECNT=4;FS=5.753;HCNT=8;MAX_ED=153;MIN_ED=133;MQ=55.56;MQ0=12;MQRankSum=-2.395;NLOD=14.16;ReadPosRankSum=0.635;TLOD=4.43;ANN=C|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*1218A>C|||||1218|,C|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132861355A>C|||||| GT:AD:AF:DP:PGT:PID 0/1:194,2:0.014:196:0|1:132861353_G_A 0/0:83,1:0.016:84:0|1:132861353_G_A | |
| chr2 132861373 . G C . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=338;ECNT=4;FS=11.596;HCNT=8;MAX_ED=153;MIN_ED=133;MQ=54.56;MQ0=14;MQRankSum=-1.12;NLOD=1.87;ReadPosRankSum=0.285;TLOD=4.38;ANN=C|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*1236G>C|||||1236|,C|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132861373G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:218,2:0.013:220:0|1:132861353_G_A 0/0:90,3:0.061:93:0|1:132861353_G_A | |
| chr2 132861935 . T C . t_lod_fstar ClippingRankSum=0;DP=315;ECNT=1;FS=19.679;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=50.86;MQ0=19;MQRankSum=-0.008;NLOD=5.56;ReadPosRankSum=-0.579;TLOD=4.91;ANN=C|downstream_gene_variant|MODIFIER|AC098826.4|ENSG00000225594|transcript|ENST00000433943|unprocessed_pseudogene||n.*1798T>C|||||1798|,C|intergenic_region|MODIFIER|AC098826.4-AC098826.5|ENSG00000225594-ENSG00000227745|intergenic_region|ENSG00000225594-ENSG00000227745|||n.132861935T>C|||||| GT:AD:AF:DP 0/1:179,6:0.045:185 0/0:90,11:0.111:101 | |
| chr2 132912341 . C T . PASS ClippingRankSum=0;DP=683;ECNT=1;FS=3.466;HCNT=19;MAX_ED=.;MIN_ED=.;MQ=53.41;MQ0=48;MQRankSum=-8.497;NLOD=19.04;ReadPosRankSum=-0.821;TLOD=27.76;ANN=T|missense_variant&splice_region_variant|MODERATE|ANKRD30BL|ENSG00000163046|transcript|ENST00000409867|protein_coding|4/6|c.508G>A|p.Ala170Thr|758/1251|508/777|170/258||,T|missense_variant&splice_region_variant|MODERATE|ANKRD30BL|ENSG00000163046|transcript|ENST00000295181|nonsense_mediated_decay|4/7|c.508G>A|p.Ala170Thr|758/1412|508/756|170/251||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|3/5|n.616G>A||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|ANKRD30BL|ENSG00000163046|transcript|ENST00000471048|processed_transcript|4/5|n.386G>A||||||,T|sequence_feature|LOW|ANKRD30BL|ENSG00000163046|repeat:ANK_4|ENST00000409867|protein_coding|4/6|c.508G>A||||||,T|sequence_feature|LOW|ANKRD30BL|ENSG00000163046|repeat:ANK_4|ENST00000295181|nonsense_mediated_decay|4/7|c.508G>A||||||,T|upstream_gene_variant|MODIFIER|RNU6-1132P|ENSG00000239108|transcript|ENST00000459214|snRNA||n.-2419G>A|||||2419|,T|upstream_gene_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000465868|processed_transcript||n.-2030G>A|||||2030|,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000481691|retained_intron|3/5|n.2760G>A|||||| GT:AD:AF:DP 0/1:385,36:0.069:421 0/0:175,18:0.076:193 | |
| chr2 132919099 . C T . PASS ClippingRankSum=0;DP=280;ECNT=1;FS=1.056;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=54.85;MQ0=9;MQRankSum=-1.732;NLOD=7.32;ReadPosRankSum=-1.67;TLOD=6.40;ANN=T|synonymous_variant|LOW|ANKRD30BL|ENSG00000163046|transcript|ENST00000409867|protein_coding|1/6|c.180G>A|p.Lys60Lys|430/1251|180/777|60/258||,T|synonymous_variant|LOW|ANKRD30BL|ENSG00000163046|transcript|ENST00000295181|nonsense_mediated_decay|1/7|c.180G>A|p.Lys60Lys|430/1412|180/756|60/251||,T|intron_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/4|n.442-4380G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000481691|retained_intron|1/5|n.228G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000471048|processed_transcript|1/5|n.58G>A|||||| GT:AD:AF:DP 0/1:171,8:0.033:179 0/0:81,6:0.049:87 | |
| chr2 133014592 . G A . germline_risk ClippingRankSum=0;DP=30;ECNT=1;FS=1.596;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=51.85;MQ0=2;MQRankSum=-4.529;NLOD=1.20;ReadPosRankSum=-1.458;TLOD=33.73;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-3714C>T|||||3714|,A|intron_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/4|n.441+510C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA|1/1|n.62C>T|||||| GT:AD:AF:DP 0/1:11,11:0.579:22 0/0:5,0:0:5 | |
| chr2 133015494 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=540;ECNT=8;FS=0;HCNT=6;MAX_ED=149;MIN_ED=27;MQ=54.74;MQ0=7;MQRankSum=-5.614;NLOD=14.89;ReadPosRankSum=0.215;TLOD=14.10;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4616C>T|||||4616|,A|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-841C>T|||||841|,A|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4407G>A|||||4407|,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/5|n.49C>T|||||| GT:AD:AF:DP 0/1:332,13:0.034:345 0/0:126,7:0.041:133 | |
| chr2 133015521 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=480;ECNT=8;FS=0;HCNT=5;MAX_ED=149;MIN_ED=27;MQ=54.37;MQ0=7;MQRankSum=-2.085;NLOD=3.39;ReadPosRankSum=2.877;TLOD=6.52;ANN=T|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4643G>A|||||4643|,T|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-868G>A|||||868|,T|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4380C>T|||||4380|,T|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/5|n.22G>A|||||| GT:AD:AF:DP:PGT:PID 0/1:306,4:0.013:310:0|1:133015521_C_T 0/0:109,5:0.057:114:0|1:133015521_C_T | |
| chr2 133015522 . C A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=477;ECNT=8;FS=15.299;HCNT=16;MAX_ED=149;MIN_ED=27;MQ=54.37;MQ0=7;MQRankSum=-6.069;NLOD=11.18;ReadPosRankSum=0.069;TLOD=50.04;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4644G>T|||||4644|,A|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-869G>T|||||869|,A|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4379C>A|||||4379|,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/5|n.21G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:290,18:0.073:308:0|1:133015522_C_A 0/0:109,5:0.048:114:0|1:133015522_C_A | |
| chr2 133015527 . G A . clustered_events;germline_risk;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=452;ECNT=8;FS=0;HCNT=5;MAX_ED=149;MIN_ED=27;MQ=54.5;MQ0=5;MQRankSum=-2.053;NLOD=1.58;ReadPosRankSum=2.947;TLOD=6.55;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4649C>T|||||4649|,A|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-874C>T|||||874|,A|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4374G>A|||||4374|,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/5|n.16C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:292,4:0.013:296:0|1:133015521_C_T 0/0:101,5:0.062:106:0|1:133015521_C_T | |
| chr2 133015539 . AT A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=424;ECNT=8;FS=18.079;HCNT=16;MAX_ED=149;MIN_ED=27;MQ=54.28;MQ0=5;MQRankSum=-5.475;NLOD=7.57;ReadPosRankSum=1.38;TLOD=58.10;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4662delA|||||4662|,A|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-887delA|||||887|,A|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4361delT|||||4361|,A|non_coding_transcript_exon_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript|1/5|n.3delA|||||| GT:AD:AF:DP:PGT:PID 0/1:257,20:0.094:277:0|1:133015522_C_A 0/0:95,5:0.056:100:0|1:133015522_C_A | |
| chr2 133015559 . A G . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=386;ECNT=8;FS=15.768;HCNT=16;MAX_ED=149;MIN_ED=27;MQ=54.99;MQ0=5;MQRankSum=-5.954;NLOD=6.37;ReadPosRankSum=3.399;TLOD=62.38;ANN=G|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4681T>C|||||4681|,G|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-906T>C|||||906|,G|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4342A>G|||||4342|,G|upstream_gene_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript||n.-17T>C|||||17|,G|intergenic_region|MODIFIER|ANKRD30BL-CDC27P1|ENSG00000163046-ENSG00000233786|intergenic_region|ENSG00000163046-ENSG00000233786|||n.133015559A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:229,21:0.107:250:0|1:133015522_C_A 0/0:89,5:0.06:94:0|1:133015522_C_A | |
| chr2 133015573 . C T . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=343;ECNT=8;FS=13.74;HCNT=16;MAX_ED=149;MIN_ED=27;MQ=55.35;MQ0=2;MQRankSum=-5.256;NLOD=6.37;ReadPosRankSum=2.9;TLOD=62.73;ANN=T|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4695G>A|||||4695|,T|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-920G>A|||||920|,T|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4328C>T|||||4328|,T|upstream_gene_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript||n.-31G>A|||||31|,T|intergenic_region|MODIFIER|ANKRD30BL-CDC27P1|ENSG00000163046-ENSG00000233786|intergenic_region|ENSG00000163046-ENSG00000233786|||n.133015573C>T|||||| GT:AD:AF:DP:PGT:PID 0/1:212,21:0.111:233:0|1:133015522_C_A 0/0:83,5:0.06:88:0|1:133015522_C_A | |
| chr2 133015643 . G A . clustered_events;multi_event_alt_allele_in_normal ClippingRankSum=0;DP=110;ECNT=8;FS=0;HCNT=10;MAX_ED=149;MIN_ED=27;MQ=57.69;MQ0=0;MQRankSum=-3.668;NLOD=2.72;ReadPosRankSum=-0.158;TLOD=32.15;ANN=A|upstream_gene_variant|MODIFIER|RNA5-8SP5|ENSG00000202174|transcript|ENST00000365304|rRNA||n.-4765C>T|||||4765|,A|upstream_gene_variant|MODIFIER|MIR663B|ENSG00000221288|transcript|ENST00000408361|miRNA||n.-990C>T|||||990|,A|upstream_gene_variant|MODIFIER|CDC27P1|ENSG00000233786|transcript|ENST00000445384|processed_pseudogene||n.-4258G>A|||||4258|,A|upstream_gene_variant|MODIFIER|ANKRD30BL|ENSG00000163046|transcript|ENST00000470729|processed_transcript||n.-101C>T|||||101|,A|intergenic_region|MODIFIER|ANKRD30BL-CDC27P1|ENSG00000163046-ENSG00000233786|intergenic_region|ENSG00000163046-ENSG00000233786|||n.133015643G>A|||||| GT:AD:AF:DP 0/1:70,11:0.132:81 0/0:23,1:0.042:24 | |
| chr2 133038681 . T C . clustered_events;germline_risk ClippingRankSum=0;DP=12;ECNT=2;FS=0;HCNT=2;MAX_ED=5;MIN_ED=5;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.602;ReadPosRankSum=0.469;TLOD=15.79;ANN=C|downstream_gene_variant|MODIFIER|AC097532.2|ENSG00000230803|transcript|ENST00000440802|lincRNA||n.*4687A>G|||||4687|,C|intergenic_region|MODIFIER|CDC27P1-AC097532.2|ENSG00000233786-ENSG00000230803|intergenic_region|ENSG00000233786-ENSG00000230803|||n.133038681T>C|||||| GT:AD:AF:DP:PGT:PID 0/1:1,7:0.8:8:0|1:133038681_T_C 0/0:4,0:0:4:0|1:133038681_T_C | |
| chr2 133038686 . A G . clustered_events;germline_risk ClippingRankSum=0;DP=10;ECNT=2;FS=0;HCNT=2;MAX_ED=5;MIN_ED=5;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.602;ReadPosRankSum=1.221;TLOD=18.88;ANN=G|downstream_gene_variant|MODIFIER|AC097532.2|ENSG00000230803|transcript|ENST00000440802|lincRNA||n.*4682T>C|||||4682|,G|intergenic_region|MODIFIER|CDC27P1-AC097532.2|ENSG00000233786-ENSG00000230803|intergenic_region|ENSG00000233786-ENSG00000230803|||n.133038686A>G|||||| GT:AD:AF:DP:PGT:PID 0/1:1,5:0.833:6:0|1:133038681_T_C 0/0:4,0:0:4:0|1:133038681_T_C | |
| chr2 133540521 . G T . t_lod_fstar ClippingRankSum=0;DP=52;ECNT=1;FS=2.385;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.91;ReadPosRankSum=1.317;TLOD=4.13;ANN=T|missense_variant|MODERATE|NCKAP5|ENSG00000176771|transcript|ENST00000317721|protein_coding|12/18|c.3863C>A|p.Thr1288Lys|3863/5730|3863/5730|1288/1909||,T|missense_variant|MODERATE|NCKAP5|ENSG00000176771|transcript|ENST00000409261|protein_coding|14/20|c.3863C>A|p.Thr1288Lys|4237/7592|3863/5730|1288/1909||,T|upstream_gene_variant|MODIFIER|NCKAP5|ENSG00000176771|transcript|ENST00000473859|processed_transcript||n.-925C>A|||||925|,T|intron_variant|MODIFIER|NCKAP5|ENSG00000176771|transcript|ENST00000409213|protein_coding|13/17|c.1092+7075C>A||||||,T|intron_variant|MODIFIER|NCKAP5|ENSG00000176771|transcript|ENST00000405974|protein_coding|11/15|c.1092+7075C>A|||||| GT:AD:AF:DP 0/1:30,3:0.08:33 0/0:19,0:0:19 | |
| chr2 135625118 . CCT C . t_lod_fstar ClippingRankSum=0;DP=76;ECNT=1;FS=3.489;HCNT=31;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.11;ReadPosRankSum=-0.298;TLOD=5.38;ANN=C|intron_variant|MODIFIER|ACMSD|ENSG00000153086|transcript|ENST00000356140|protein_coding|5/9|c.487-17_487-16delTC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|ACMSD|ENSG00000153086|transcript|ENST00000485893|retained_intron|5/7|n.554-17_554-16delTC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|ACMSD|ENSG00000153086|transcript|ENST00000283054|protein_coding|4/8|c.313-17_313-16delTC||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|ACMSD|ENSG00000153086|transcript|ENST00000392928|protein_coding|5/9|c.313-17_313-16delTC||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|CCNT2-AS1|ENSG00000224043|transcript|ENST00000537615|antisense|5/5|n.488_489delAG||||||,C|non_coding_transcript_exon_variant|MODIFIER|CCNT2-AS1|ENSG00000224043|transcript|ENST00000392929|antisense|3/4|n.396_397delAG||||||,C|non_coding_transcript_exon_variant|MODIFIER|CCNT2-AS1|ENSG00000224043|transcript|ENST00000413962|antisense|3/3|n.404_405delAG||||||,C|non_coding_transcript_exon_variant|MODIFIER|CCNT2-AS1|ENSG00000224043|transcript|ENST00000428857|antisense|4/4|n.560_561delAG|||||| GT:AD:AF:DP 0/1:52,4:0.064:56 0/0:18,0:0:18 | |
| chr2 135745722 . A G . PASS ClippingRankSum=0;DP=31;ECNT=1;FS=1.561;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.41;ReadPosRankSum=-1.042;TLOD=35.65;ANN=G|synonymous_variant|LOW|MAP3K19|ENSG00000176601|transcript|ENST00000375845|protein_coding|7/10|c.720T>C|p.Ser240Ser|751/4377|720/3987|240/1328||,G|synonymous_variant|LOW|MAP3K19|ENSG00000176601|transcript|ENST00000358371|protein_coding|5/8|c.381T>C|p.Ser127Ser|412/3719|381/3648|127/1215||,G|synonymous_variant|LOW|MAP3K19|ENSG00000176601|transcript|ENST00000392915|protein_coding|7/10|c.771T>C|p.Ser257Ser|891/4350|771/3459|257/1152||,G|5_prime_UTR_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000315513|protein_coding|7/10|c.-2850T>C|||||6829|,G|upstream_gene_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000478805|retained_intron||n.-4673T>C|||||4673|,G|upstream_gene_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000437365|protein_coding||c.-1111T>C|||||1111|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000468155|retained_intron||n.*3189T>C|||||3189|,G|intron_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000392917|protein_coding|6/7|c.618+3385T>C||||||,G|intron_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000375844|protein_coding|6/8|c.618+3385T>C||||||,G|intron_variant|MODIFIER|MAP3K19|ENSG00000176601|transcript|ENST00000392918|protein_coding|6/8|c.618+3385T>C|||||| GT:AD:AF:DP 0/1:3,17:0.8:20 0/0:11,0:0:11 | |
| chr2 136513161 . G A . PASS ClippingRankSum=0;DP=180;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.02;ReadPosRankSum=-2.463;TLOD=108.83;ANN=A|synonymous_variant|LOW|UBXN4|ENSG00000144224|transcript|ENST00000272638|protein_coding|5/13|c.408G>A|p.Ala136Ala|719/4006|408/1527|136/508||,A|3_prime_UTR_variant|MODIFIER|UBXN4|ENSG00000144224|transcript|ENST00000426921|nonsense_mediated_decay|3/4|c.*62G>A|||||62|,A|3_prime_UTR_variant|MODIFIER|UBXN4|ENSG00000144224|transcript|ENST00000416538|nonsense_mediated_decay|4/5|c.*711G>A|||||1950|,A|downstream_gene_variant|MODIFIER|UBXN4|ENSG00000144224|transcript|ENST00000415164|protein_coding||c.*1403G>A|||||1403|WARNING_TRANSCRIPT_INCOMPLETE,A|non_coding_transcript_exon_variant|MODIFIER|UBXN4|ENSG00000144224|transcript|ENST00000470687|retained_intron|4/4|n.482G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|UBXN4|ENSG00000144224|transcript|ENST00000490163|processed_transcript|2/9|n.201G>A|||||| GT:AD:AF:DP 0/1:71,66:0.482:137 0/0:43,0:0:43 | |
| chr2 136567084 . C T . t_lod_fstar ClippingRankSum=0;DP=89;ECNT=1;FS=3.059;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.42;ReadPosRankSum=-1.752;TLOD=4.16;ANN=T|missense_variant|MODERATE|LCT|ENSG00000115850|transcript|ENST00000264162|protein_coding|8/17|c.2833G>A|p.Asp945Asn|2844/6279|2833/5784|945/1927||,T|missense_variant|MODERATE|LCT|ENSG00000115850|transcript|ENST00000452974|nonsense_mediated_decay|2/7|c.1129G>A|p.Asp377Asn|1129/3508|1129/3012|377/1003||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000200664|transcript|ENST00000363794|misc_RNA||n.*655G>A|||||655| GT:AD:AF:DP 0/1:68,1:0.033:69 0/0:20,0:0:20 | |
| chr2 141202032 . GGA G . PASS ClippingRankSum=0;DP=275;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=5.164;NLOD=9.14;ReadPosRankSum=-1.257;TLOD=6.42;ANN=G|intron_variant|MODIFIER|LRP1B|ENSG00000168702|transcript|ENST00000389484|protein_coding|64/90|c.10175-16_10175-15delTC|||||| GT:AD:AF:DP 0/1:170,7:0.042:177 0/0:72,2:0.038:74 | |
| chr2 145147292 . G C . t_lod_fstar ClippingRankSum=0;DP=72;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.12;ReadPosRankSum=-0.589;TLOD=4.10;ANN=C|missense_variant|MODERATE|ZEB2|ENSG00000169554|transcript|ENST00000303660|protein_coding|10/10|c.3371C>G|p.Ser1124Trp|3504/5215|3371/3645|1124/1214||,C|missense_variant|MODERATE|ZEB2|ENSG00000169554|transcript|ENST00000558170|protein_coding|10/10|c.3371C>G|p.Ser1124Trp|4556/10200|3371/3645|1124/1214||,C|missense_variant|MODERATE|ZEB2|ENSG00000169554|transcript|ENST00000409487|protein_coding|10/10|c.3371C>G|p.Ser1124Trp|3559/5283|3371/3645|1124/1214||,C|missense_variant|MODERATE|ZEB2|ENSG00000169554|transcript|ENST00000539609|protein_coding|9/9|c.3299C>G|p.Ser1100Trp|3549/5257|3299/3573|1100/1190||,C|sequence_feature|MODERATE|ZEB2|ENSG00000169554|modified-residue:Phosphoserine|ENST00000409487|protein_coding|10/10|c.3371C>G||||||,C|sequence_feature|MODERATE|ZEB2|ENSG00000169554|modified-residue:Phosphoserine|ENST00000539609|protein_coding|9/9|c.3299C>G||||||,C|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000419938|protein_coding|3/3|c.581-843C>G||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:49,1:0.049:50 0/0:22,0:0:22 | |
| chr2 145188050 . GAC G . PASS ClippingRankSum=0;DP=326;ECNT=1;FS=2.424;HCNT=25;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.53;ReadPosRankSum=-0.658;TLOD=8.12;ANN=G|upstream_gene_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000419938|protein_coding||c.-461_-460delGT|||||458|WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000303660|protein_coding|2/9|c.74-459_74-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000558170|protein_coding|2/9|c.74-459_74-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000409487|protein_coding|2/9|c.74-459_74-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000539609|protein_coding|2/8|c.74-459_74-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000427902|protein_coding|2/7|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000392861|protein_coding|2/7|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_NO_STOP_CODON,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000440875|protein_coding|1/3|c.31+53_31+54delGT||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000409211|protein_coding|2/3|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000431672|protein_coding|1/2|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000472146|retained_intron|2/2|n.324-459_324-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000465308|retained_intron|3/3|n.699-459_699-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000461784|retained_intron|1/1|n.281-459_281-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000560384|retained_intron|1/1|n.414-459_414-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000476394|retained_intron|2/2|n.178-459_178-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000434448|processed_transcript|3/3|n.314-459_314-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000479735|processed_transcript|1/1|n.305-459_305-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000435831|protein_coding|2/2|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000453352|processed_transcript|3/3|n.381-459_381-458delGT||||||,G|intron_variant|MODIFIER|ZEB2|ENSG00000169554|transcript|ENST00000444559|protein_coding|3/3|c.74-459_74-458delGT||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:213,9:0.035:222 0/0:90,4:0.046:94 | |
| chr2 148683685 . TA T . PASS ClippingRankSum=0;DP=301;ECNT=1;FS=4.875;HCNT=31;MAX_ED=.;MIN_ED=.;MQ=60.07;MQ0=0;MQRankSum=1.801;NLOD=16.05;ReadPosRankSum=0.746;TLOD=118.90;ANN=T|frameshift_variant|HIGH|ACVR2A|ENSG00000121989|transcript|ENST00000241416|protein_coding|10/11|c.1310delA|p.Lys437fs|1946/5728|1310/1542|437/513||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ACVR2A|ENSG00000121989|transcript|ENST00000535787|protein_coding|10/11|c.986delA|p.Lys329fs|1382/1956|986/1218|329/405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ACVR2A|ENSG00000121989|transcript|ENST00000404590|protein_coding|11/12|c.1310delA|p.Lys437fs|1480/2367|1310/1542|437/513||INFO_REALIGN_3_PRIME,T|downstream_gene_variant|MODIFIER|ORC4|ENSG00000115947|transcript|ENST00000392857|protein_coding||c.*9393delT|||||4282|,T|non_coding_transcript_exon_variant|MODIFIER|ACVR2A|ENSG00000121989|transcript|ENST00000495775|processed_transcript|1/2|n.438delA||||||INFO_REALIGN_3_PRIME;LOF=(ACVR2A|ENSG00000121989|7|0.43) GT:AD:AF:DP 0/1:99,107:0.524:206 0/0:77,0:0:77 | |
| chr2 149855032 . G A . t_lod_fstar ClippingRankSum=0;DP=49;ECNT=1;FS=5.636;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=4.51;ReadPosRankSum=0.906;TLOD=4.13;ANN=A|upstream_gene_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000482151|retained_intron||n.-1417G>A|||||1417|,A|intron_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000435030|protein_coding|19/25|c.2210+9G>A||||||,A|intron_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000414838|protein_coding|17/23|c.1925+9G>A||||||,A|intron_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000464066|processed_transcript|12/19|n.1557+9G>A||||||,A|intron_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000397413|protein_coding|12/18|c.1514+9G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|KIF5C|ENSG00000168280|transcript|ENST00000460377|retained_intron|6/6|n.1977G>A|||||| GT:AD:AF:DP 0/1:26,3:0.1:29 0/0:20,0:0:20 | |
| chr2 152322038 . G T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=81;ECNT=4;FS=11.942;HCNT=51;MAX_ED=4;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.22;ReadPosRankSum=-0.475;TLOD=5.39;ANN=T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000243326|protein_coding|29/35|c.6004G>T|p.Gly2002*|6487/15003|6004/7419|2002/2472||,T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000444746|protein_coding|30/36|c.6004G>T|p.Gly2002*|6165/7897|6004/7419|2002/2472||,T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000453091|protein_coding|30/35|c.6004G>T|p.Gly2002*|6165/8053|6004/7341|2002/2446||,T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000428287|protein_coding|30/35|c.6004G>T|p.Gly2002*|6068/7722|6004/7341|2002/2446||,T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000430328|protein_coding|29/34|c.6004G>T|p.Gly2002*|6338/7992|6004/7341|2002/2446||,T|stop_gained|HIGH|RIF1|ENSG00000080345|transcript|ENST00000454583|nonsense_mediated_decay|1/14|c.823G>T|p.Gly275*|825/3552|823/2238|275/745||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(RIF1|ENSG00000080345|14|0.43);NMD=(RIF1|ENSG00000080345|14|0.43) GT:AD:AF:DP:PGT:PID 0/1:58,2:0.042:60:0|1:152322038_G_T 0/0:20,1:0.053:21:0|1:152322038_G_T | |
| chr2 152322039 . G T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=79;ECNT=4;FS=12.026;HCNT=51;MAX_ED=4;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.52;ReadPosRankSum=-0.565;TLOD=5.35;ANN=T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000243326|protein_coding|29/35|c.6005G>T|p.Gly2002Val|6488/15003|6005/7419|2002/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000444746|protein_coding|30/36|c.6005G>T|p.Gly2002Val|6166/7897|6005/7419|2002/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000453091|protein_coding|30/35|c.6005G>T|p.Gly2002Val|6166/8053|6005/7341|2002/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000428287|protein_coding|30/35|c.6005G>T|p.Gly2002Val|6069/7722|6005/7341|2002/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000430328|protein_coding|29/34|c.6005G>T|p.Gly2002Val|6339/7992|6005/7341|2002/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000454583|nonsense_mediated_decay|1/14|c.824G>T|p.Gly275Val|826/3552|824/2238|275/745||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:56,2:0.04:58:0|1:152322038_G_T 0/0:20,1:0.05:21:0|1:152322038_G_T | |
| chr2 152322041 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=79;ECNT=4;FS=11.612;HCNT=51;MAX_ED=4;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.52;ReadPosRankSum=-0.715;TLOD=5.34;ANN=T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000243326|protein_coding|29/35|c.6007A>T|p.Asn2003Tyr|6490/15003|6007/7419|2003/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000444746|protein_coding|30/36|c.6007A>T|p.Asn2003Tyr|6168/7897|6007/7419|2003/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000453091|protein_coding|30/35|c.6007A>T|p.Asn2003Tyr|6168/8053|6007/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000428287|protein_coding|30/35|c.6007A>T|p.Asn2003Tyr|6071/7722|6007/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000430328|protein_coding|29/34|c.6007A>T|p.Asn2003Tyr|6341/7992|6007/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000454583|nonsense_mediated_decay|1/14|c.826A>T|p.Asn276Tyr|828/3552|826/2238|276/745||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:55,2:0.039:57:0|1:152322038_G_T 0/0:21,1:0.05:22:0|1:152322038_G_T | |
| chr2 152322042 . A T . clustered_events;germline_risk;multi_event_alt_allele_in_normal;t_lod_fstar ClippingRankSum=0;DP=77;ECNT=4;FS=11.687;HCNT=51;MAX_ED=4;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.52;ReadPosRankSum=-0.921;TLOD=5.34;ANN=T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000243326|protein_coding|29/35|c.6008A>T|p.Asn2003Ile|6491/15003|6008/7419|2003/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000444746|protein_coding|30/36|c.6008A>T|p.Asn2003Ile|6169/7897|6008/7419|2003/2472||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000453091|protein_coding|30/35|c.6008A>T|p.Asn2003Ile|6169/8053|6008/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000428287|protein_coding|30/35|c.6008A>T|p.Asn2003Ile|6072/7722|6008/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000430328|protein_coding|29/34|c.6008A>T|p.Asn2003Ile|6342/7992|6008/7341|2003/2446||,T|missense_variant|MODERATE|RIF1|ENSG00000080345|transcript|ENST00000454583|nonsense_mediated_decay|1/14|c.827A>T|p.Asn276Ile|829/3552|827/2238|276/745||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP:PGT:PID 0/1:54,2:0.039:56:0|1:152322038_G_T 0/0:20,1:0.05:21:0|1:152322038_G_T | |
| chr2 152409876 . G T . t_lod_fstar ClippingRankSum=0;DP=101;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.22;ReadPosRankSum=-1.26;TLOD=4.34;ANN=T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000397345|protein_coding|127/181|c.19731+36C>A||||||,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000409198|protein_coding|100/149|c.14628+36C>A||||||,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000427231|protein_coding|127/181|c.19731+36C>A||||||,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000413693|protein_coding|27/73|c.3921+36C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000172853|protein_coding|99/148|c.14628+36C>A||||||,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000603639|protein_coding|125/179|c.19731+36C>A||||||,T|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000604864|protein_coding|125/179|c.19731+36C>A|||||| GT:AD:AF:DP 0/1:66,4:0.056:70 0/0:30,0:0:30 | |
| chr2 152482168 . A G . t_lod_fstar ClippingRankSum=0;DP=124;ECNT=1;FS=0;HCNT=28;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.83;ReadPosRankSum=-0.028;TLOD=4.07;ANN=G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000397345|protein_coding|70/181|c.10348-16T>C||||||,G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000409198|protein_coding|67/149|c.9619-16T>C||||||,G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000427231|protein_coding|70/181|c.10348-16T>C||||||,G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000172853|protein_coding|66/148|c.9619-16T>C||||||,G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000603639|protein_coding|68/179|c.10348-16T>C||||||,G|intron_variant|MODIFIER|NEB|ENSG00000183091|transcript|ENST00000604864|protein_coding|68/179|c.10348-16T>C|||||| GT:AD:AF:DP 0/1:89,1:0.032:90 0/0:33,0:0:33 | |
| chr2 152695191 . C T . t_lod_fstar ClippingRankSum=0;DP=241;ECNT=1;FS=4.219;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.79;ReadPosRankSum=-1.046;TLOD=5.96;ANN=T|3_prime_UTR_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000539935|protein_coding|14/14|c.*442G>A|||||442|,T|3_prime_UTR_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000360283|protein_coding|13/13|c.*442G>A|||||442|,T|3_prime_UTR_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000439467|protein_coding|13/13|c.*442G>A|||||442|WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000534999|protein_coding|13/13|c.*442G>A|||||442|,T|downstream_gene_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000397327|protein_coding||c.*442G>A|||||7|,T|downstream_gene_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000427385|protein_coding||c.*442G>A|||||137|,T|downstream_gene_variant|MODIFIER|CACNB4|ENSG00000182389|transcript|ENST00000201943|protein_coding||c.*442G>A|||||437| GT:AD:AF:DP 0/1:164,9:0.053:173 0/0:56,3:0.056:59 | |
| chr2 162281205 . GTGGA G . t_lod_fstar ClippingRankSum=0;DP=189;ECNT=1;FS=5.538;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.71;ReadPosRankSum=-0.293;TLOD=4.85;ANN=G|splice_donor_variant&splice_region_variant&intron_variant&non_coding_transcript_exon_variant|HIGH|SLC4A10|ENSG00000144290|transcript|ENST00000482861|processed_transcript|1/4|n.383_385+1delATGG||||||INFO_REALIGN_3_PRIME,G|splice_donor_variant&splice_region_variant&intron_variant&non_coding_transcript_exon_variant|HIGH|SLC4A10|ENSG00000144290|transcript|ENST00000605990|processed_transcript|1/5|n.342_344+1delATGG||||||INFO_REALIGN_3_PRIME,G|3_prime_UTR_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000389554|protein_coding|6/6|c.*487_*490delATGG|||||487|INFO_REALIGN_3_PRIME,G|upstream_gene_variant|MODIFIER|AC009487.4|ENSG00000224076|transcript|ENST00000444164|antisense||n.-1563_-1560delTCCA|||||1560|,G|upstream_gene_variant|MODIFIER|AC009487.4|ENSG00000224076|transcript|ENST00000437683|antisense||n.-1121_-1118delTCCA|||||1118|,G|upstream_gene_variant|MODIFIER|SLC4A10|ENSG00000144290|transcript|ENST00000606386|processed_transcript||n.-2758_-2755delTGGA|||||2758|,G|downstream_gene_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000463544|retained_intron||n.*810_*813delTGGA|||||810|,G|downstream_gene_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000411412|protein_coding||c.*919_*922delTGGA|||||919|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000410035|protein_coding||c.*468_*471delTGGA|||||409|,G|downstream_gene_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000477804|processed_transcript||n.*1010_*1013delTGGA|||||1010|,G|downstream_gene_variant|MODIFIER|TBR1|ENSG00000136535|transcript|ENST00000489530|processed_transcript||n.*1240_*1243delTGGA|||||1240|,G|intron_variant|MODIFIER|AC009487.5|ENSG00000251621|transcript|ENST00000505579|prime3_overlapping_ncrna|1/1|n.226+474_226+477delATGG||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:122,2:0.022:124 0/0:45,1:0.029:46 | |
| chr2 163054893 . C T . t_lod_fstar ClippingRankSum=0;DP=92;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=1.074;TLOD=4.51;ANN=T|upstream_gene_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000497414|retained_intron||n.-3346G>A|||||3346|,T|downstream_gene_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000465088|retained_intron||n.*241G>A|||||241|,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000188790|protein_coding|16/25|c.1402+374G>A||||||,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000422436|nonsense_mediated_decay|1/12|c.71-85G>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000443424|protein_coding|15/24|c.1327+374G>A||||||,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000465424|retained_intron|1/2|n.86+374G>A|||||| GT:AD:AF:DP 0/1:67,1:0.043:68 0/0:24,0:0:24 | |
| chr2 163078167 . G T . t_lod_fstar ClippingRankSum=0;DP=154;ECNT=1;FS=1.79;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60.07;MQ0=0;MQRankSum=-0.147;NLOD=9.03;ReadPosRankSum=-1.239;TLOD=5.01;ANN=T|3_prime_UTR_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000450031|nonsense_mediated_decay|6/7|c.*40C>A|||||40|,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000188790|protein_coding|6/25|c.414-1732C>A||||||,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000443424|protein_coding|5/24|c.339-1732C>A||||||,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000480838|retained_intron|5/10|n.401-1732C>A||||||,T|intron_variant|MODIFIER|FAP|ENSG00000078098|transcript|ENST00000447386|protein_coding|5/6|c.351-1732C>A||||||WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:107,5:0.038:112 0/0:42,0:0:42 | |
| chr2 165947630 . G T . t_lod_fstar ClippingRankSum=0;DP=274;ECNT=1;FS=0;HCNT=31;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.91;ReadPosRankSum=-0.821;TLOD=4.11;ANN=T|missense_variant|MODERATE|SCN3A|ENSG00000153253|transcript|ENST00000283254|protein_coding|28/28|c.5033C>A|p.Ala1678Asp|5501/9091|5033/6003|1678/2000||,T|missense_variant|MODERATE|SCN3A|ENSG00000153253|transcript|ENST00000360093|protein_coding|28/28|c.5033C>A|p.Ala1678Asp|5525/9123|5033/6003|1678/2000||,T|missense_variant|MODERATE|SCN3A|ENSG00000153253|transcript|ENST00000409101|protein_coding|28/28|c.4886C>A|p.Ala1629Asp|5197/6599|4886/5856|1629/1951||,T|missense_variant|MODERATE|SCN3A|ENSG00000153253|transcript|ENST00000540861|protein_coding|3/3|c.482C>A|p.Ala161Asp|759/1908|482/1452|161/483||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|AC013463.2|ENSG00000236283|transcript|ENST00000431341|antisense|4/4|n.462G>T||||||,T|downstream_gene_variant|MODIFIER|SCN3A|ENSG00000153253|transcript|ENST00000465043|processed_transcript||n.*1136C>A|||||1136|,T|downstream_gene_variant|MODIFIER|SCN3A|ENSG00000153253|transcript|ENST00000471697|retained_intron||n.*4391C>A|||||4391| GT:AD:AF:DP 0/1:185,5:0.022:190 0/0:84,0:0:84 | |
| chr2 166929299 . T TTTCC . PASS ClippingRankSum=0;DP=177;ECNT=1;FS=4.076;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=59.5;MQ0=1;MQRankSum=0;NLOD=4.40;ReadPosRankSum=0.505;TLOD=7.59;ANN=TTTCC|downstream_gene_variant|MODIFIER|SCN1A|ENSG00000144285|transcript|ENST00000507401|retained_intron||n.*509_*512dupGGAA|||||512|,TTTCC|intron_variant|MODIFIER|SCN1A|ENSG00000144285|transcript|ENST00000303395|protein_coding|1/25|c.264+565_264+568dupGGAA||||||,TTTCC|intron_variant|MODIFIER|AC010127.3|ENSG00000236107|transcript|ENST00000595647|antisense|3/6|n.425-19739_425-19736dupTTCC||||||INFO_REALIGN_3_PRIME,TTTCC|intron_variant|MODIFIER|SCN1A|ENSG00000144285|transcript|ENST00000423058|protein_coding|1/25|c.264+565_264+568dupGGAA||||||,TTTCC|intron_variant|MODIFIER|SCN1A|ENSG00000144285|transcript|ENST00000375405|protein_coding|1/25|c.264+565_264+568dupGGAA||||||,TTTCC|intron_variant|MODIFIER|SCN1A|ENSG00000144285|transcript|ENST00000409050|protein_coding|1/25|c.264+565_264+568dupGGAA||||||,TTTCC|intron_variant|MODIFIER|AC010127.3|ENSG00000236107|transcript|ENST00000599041|antisense|1/6|n.67-2474_67-2471dupTTCC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:67,7:0.25:74 0/0:17,0:0:17 | |
| chr2 167055540 . G T . t_lod_fstar ClippingRankSum=0;DP=284;ECNT=1;FS=1.993;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=18.05;ReadPosRankSum=0.702;TLOD=4.24;ANN=T|missense_variant|MODERATE|SCN9A|ENSG00000169432|transcript|ENST00000303354|protein_coding|27/27|c.5612C>A|p.Ala1871Glu|5953/9787|5612/5970|1871/1989||,T|missense_variant|MODERATE|SCN9A|ENSG00000169432|transcript|ENST00000409672|protein_coding|27/27|c.5576C>A|p.Ala1859Glu|5923/9768|5576/5934|1859/1977||,T|missense_variant|MODERATE|SCN9A|ENSG00000169432|transcript|ENST00000375387|protein_coding|27/27|c.5612C>A|p.Ala1871Glu|5953/9787|5612/5970|1871/1989||,T|missense_variant|MODERATE|SCN9A|ENSG00000169432|transcript|ENST00000409435|protein_coding|26/26|c.5609C>A|p.Ala1870Glu|5609/5967|5609/5967|1870/1988||,T|intron_variant|MODIFIER|AC010127.3|ENSG00000236107|transcript|ENST00000447809|antisense|3/11|n.432-609G>T|||||| GT:AD:AF:DP 0/1:201,4:0.021:205 0/0:79,0:0:79 | |
| chr2 167133782 . G T . t_lod_fstar ClippingRankSum=0;DP=253;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.71;ReadPosRankSum=0.208;TLOD=4.34;ANN=T|stop_gained|HIGH|SCN9A|ENSG00000169432|transcript|ENST00000303354|protein_coding|16/27|c.2588C>A|p.Ser863*|2929/9787|2588/5970|863/1989||,T|stop_gained|HIGH|SCN9A|ENSG00000169432|transcript|ENST00000409672|protein_coding|16/27|c.2552C>A|p.Ser851*|2899/9768|2552/5934|851/1977||,T|stop_gained|HIGH|SCN9A|ENSG00000169432|transcript|ENST00000375387|protein_coding|16/27|c.2588C>A|p.Ser863*|2929/9787|2588/5970|863/1989||,T|stop_gained|HIGH|SCN9A|ENSG00000169432|transcript|ENST00000409435|protein_coding|15/26|c.2585C>A|p.Ser862*|2585/5967|2585/5967|862/1988||,T|downstream_gene_variant|MODIFIER|SCN9A|ENSG00000169432|transcript|ENST00000452182|protein_coding||c.*4488C>A|||||4488|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|SCN9A|ENSG00000169432|transcript|ENST00000454569|protein_coding||c.*4488C>A|||||4488|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|AC010127.3|ENSG00000236107|transcript|ENST00000447809|antisense|8/11|n.1029+25G>T||||||;LOF=(SCN9A|ENSG00000169432|7|0.57);NMD=(SCN9A|ENSG00000169432|7|0.57) GT:AD:AF:DP 0/1:170,5:0.025:175 0/0:77,0:0:77 | |
| chr2 167285775 . G T . t_lod_fstar ClippingRankSum=0;DP=431;ECNT=1;FS=3.166;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=24.97;ReadPosRankSum=-1.035;TLOD=4.01;ANN=T|missense_variant|MODERATE|SCN7A|ENSG00000136546|transcript|ENST00000409855|protein_coding|16/25|c.2602C>A|p.Gln868Lys|2729/7183|2602/5049|868/1682||,T|3_prime_UTR_variant|MODIFIER|SCN7A|ENSG00000136546|transcript|ENST00000424326|nonsense_mediated_decay|17/26|c.*407C>A|||||3450|,T|downstream_gene_variant|MODIFIER|SCN7A|ENSG00000136546|transcript|ENST00000419992|protein_coding||c.*3056C>A|||||3056|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:307,4:0.014:311 0/0:120,0:0:120 | |
| chr2 168101888 . G T . t_lod_fstar ClippingRankSum=0;DP=227;ECNT=1;FS=0;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.15;ReadPosRankSum=-1.339;TLOD=4.08;ANN=T|missense_variant|MODERATE|XIRP2|ENSG00000163092|transcript|ENST00000295237|protein_coding|8/10|c.3986G>T|p.Gly1329Val|3986/12582|3986/10650|1329/3549||,T|missense_variant|MODERATE|XIRP2|ENSG00000163092|transcript|ENST00000409195|protein_coding|9/11|c.3986G>T|p.Gly1329Val|4075/12675|3986/10650|1329/3549||,T|missense_variant|MODERATE|XIRP2|ENSG00000163092|transcript|ENST00000409273|protein_coding|7/9|c.3320G>T|p.Gly1107Val|3673/12269|3320/9984|1107/3327||,T|intron_variant|MODIFIER|XIRP2|ENSG00000163092|transcript|ENST00000409043|protein_coding|8/9|c.1176+3468G>T||||||,T|intron_variant|MODIFIER|XIRP2|ENSG00000163092|transcript|ENST00000409728|protein_coding|9/10|c.1275+3468G>T||||||,T|intron_variant|MODIFIER|XIRP2|ENSG00000163092|transcript|ENST00000409756|protein_coding|7/8|c.1176+3468G>T||||||,T|intron_variant|MODIFIER|XIRP2|ENSG00000163092|transcript|ENST00000420519|protein_coding|8/9|c.1275+3468G>T||||||,T|intron_variant|MODIFIER|XIRP2|ENSG00000163092|transcript|ENST00000409605|protein_coding|6/7|c.510+3468G>T|||||| GT:AD:AF:DP 0/1:148,5:0.029:153 0/0:73,0:0:73 | |
| chr2 168812114 . TTGC T . t_lod_fstar ClippingRankSum=0;DP=134;ECNT=1;FS=2.984;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.30;ReadPosRankSum=-0.313;TLOD=5.30;ANN=T|intron_variant|MODIFIER|STK39|ENSG00000198648|transcript|ENST00000355999|protein_coding|17/17|c.1564-37_1564-35delGCA||||||,T|intron_variant|MODIFIER|STK39|ENSG00000198648|transcript|ENST00000487143|processed_transcript|8/8|n.664-37_664-35delGCA|||||| GT:AD:AF:DP 0/1:82,2:0.038:84 0/0:32,0:0:32 | |
| chr2 169628941 . G T . t_lod_fstar ClippingRankSum=0;DP=285;ECNT=1;FS=0;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.56;ReadPosRankSum=-1.444;TLOD=4.54;ANN=T|3_prime_UTR_variant|MODIFIER|CERS6|ENSG00000172292|transcript|ENST00000392687|protein_coding|11/11|c.*2769G>T|||||2769|,T|3_prime_UTR_variant|MODIFIER|CERS6|ENSG00000172292|transcript|ENST00000305747|protein_coding|10/10|c.*2769G>T|||||2769|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000594941|antisense||n.*1924C>A|||||1924|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000609665|antisense||n.*1929C>A|||||1929|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000600693|antisense||n.*1967C>A|||||1967|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000599361|antisense||n.*1968C>A|||||1968|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000609766|antisense||n.*1988C>A|||||1988|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000607993|antisense||n.*2018C>A|||||2018|,T|downstream_gene_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000599755|antisense||n.*2390C>A|||||2390|,T|non_coding_transcript_exon_variant|MODIFIER|CERS6-AS1|ENSG00000227617|transcript|ENST00000425636|antisense|3/3|n.2412C>A|||||| GT:AD:AF:DP 0/1:187,3:0.023:190 0/0:95,0:0:95 | |
| chr2 169836326 . AC A . t_lod_fstar ClippingRankSum=0;DP=57;ECNT=1;FS=6.931;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=59.52;MQ0=0;MQRankSum=0;NLOD=5.70;ReadPosRankSum=-1.336;TLOD=4.32;ANN=A|intron_variant|MODIFIER|ABCB11|ENSG00000073734|transcript|ENST00000263817|protein_coding|11/27|c.1197+49delG|||||| GT:AD:AF:DP 0/1:32,4:0.086:36 0/0:20,0:0:20 | |
| chr2 172374084 . AGCC A . t_lod_fstar ClippingRankSum=0;DP=124;ECNT=1;FS=0;HCNT=28;MAX_ED=.;MIN_ED=.;MQ=56.66;MQ0=0;MQRankSum=1.974;NLOD=9.63;ReadPosRankSum=2.001;TLOD=5.30;ANN=A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000321348|protein_coding||c.-4971_-4969delGCC|||||4773|,A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000409484|protein_coding||c.-4698_-4696delGCC|||||4672|,A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000468308|processed_transcript||n.-4773_-4771delGCC|||||4773|,A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000375252|protein_coding||c.-4971_-4969delGCC|||||4902|,A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000474182|processed_transcript||n.-4935_-4933delGCC|||||4935|,A|upstream_gene_variant|MODIFIER|CYBRD1|ENSG00000071967|transcript|ENST00000494587|processed_transcript||n.-4936_-4934delGCC|||||4936|,A|non_coding_transcript_exon_variant|MODIFIER|AC007969.5|ENSG00000233762|transcript|ENST00000397084|processed_pseudogene|1/1|n.146_148delGGC||||||,A|non_coding_transcript_exon_variant|MODIFIER|AC007969.5|ENSG00000233762|transcript|ENST00000433675|processed_pseudogene|1/1|n.140_142delGGC|||||| GT:AD:AF:DP 0/1:72,3:0.038:75 0/0:44,0:0:44 | |
| chr2 172965607 . G T . t_lod_fstar ClippingRankSum=0;DP=617;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=45.09;ReadPosRankSum=0.494;TLOD=4.02;ANN=T|synonymous_variant|LOW|DLX2|ENSG00000115844|transcript|ENST00000234198|protein_coding|3/3|c.651C>A|p.Pro217Pro|1013/2453|651/987|217/328||,T|3_prime_UTR_variant|MODIFIER|DLX2|ENSG00000115844|transcript|ENST00000466293|protein_coding|2/2|c.*514C>A|||||514|,T|upstream_gene_variant|MODIFIER|AC104801.1|ENSG00000236651|transcript|ENST00000448117|lincRNA||n.-2127G>T|||||2127| GT:AD:AF:DP 0/1:391,4:0.011:395 0/0:220,0:0:220 | |
| chr2 173850273 . C T . t_lod_fstar ClippingRankSum=0;DP=84;ECNT=1;FS=1.704;HCNT=55;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.02;ReadPosRankSum=1.519;TLOD=5.61;ANN=T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000397081|protein_coding|12/30|c.1150+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000264111|protein_coding|12/30|c.1147+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000409036|protein_coding|12/27|c.1150+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000397087|protein_coding|9/27|c.718+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000538974|protein_coding|8/26|c.637+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000540783|protein_coding|9/27|c.691+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000539331|protein_coding|9/27|c.691+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000473043|processed_transcript|8/10|n.735+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000535187|protein_coding|6/24|c.490+52C>T||||||,T|intron_variant|MODIFIER|RAPGEF4|ENSG00000091428|transcript|ENST00000459852|processed_transcript|3/3|n.482+52C>T|||||| GT:AD:AF:DP 0/1:54,6:0.075:60 0/0:24,0:0:24 | |
| chr2 174829845 . AGCG A . t_lod_fstar ClippingRankSum=0;DP=280;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.65;ReadPosRankSum=2.033;TLOD=4.53;ANN=A|upstream_gene_variant|MODIFIER|RP11-394I13.2|ENSG00000271151|transcript|ENST00000605739|lincRNA||n.-3233_-3231delGCG|||||3233|,A|upstream_gene_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000418194|protein_coding||c.-1285_-1283delCGC|||||899|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000416195|protein_coding||c.-569_-567delCGC|||||565|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000483084|processed_transcript||n.-1741_-1739delCGC|||||1739|,A|upstream_gene_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000490182|processed_transcript||n.-235_-233delCGC|||||233|,A|intron_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000310015|protein_coding|1/6|c.7+45_7+47delCGC||||||,A|intron_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000455789|protein_coding|1/5|c.-30+45_-30+47delCGC||||||,A|intron_variant|MODIFIER|SP3|ENSG00000172845|transcript|ENST00000462904|processed_transcript|1/1|n.123+68_123+70delCGC|||||| GT:AD:AF:DP 0/1:190,3:0.016:193 0/0:80,2:0.018:82 | |
| chr2 175006680 . G T . PASS ClippingRankSum=0;DP=182;ECNT=1;FS=24.113;HCNT=96;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.20;ReadPosRankSum=-0.359;TLOD=7.60;ANN=T|missense_variant|MODERATE|OLA1|ENSG00000138430|transcript|ENST00000409546|protein_coding|5/11|c.482C>A|p.Pro161His|1113/2071|482/1251|161/416||,T|missense_variant|MODERATE|OLA1|ENSG00000138430|transcript|ENST00000284719|protein_coding|5/11|c.422C>A|p.Pro141His|669/4417|422/1191|141/396||,T|missense_variant|MODERATE|OLA1|ENSG00000138430|transcript|ENST00000428402|protein_coding|5/8|c.422C>A|p.Pro141His|446/1270|422/837|141/278||,T|5_prime_UTR_variant|MODIFIER|OLA1|ENSG00000138430|transcript|ENST00000344357|protein_coding|4/10|c.-53C>A|||||53|,T|5_prime_UTR_variant|MODIFIER|OLA1|ENSG00000138430|transcript|ENST00000429575|protein_coding|2/5|c.-53C>A|||||53|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:126,4:0.033:130 0/0:49,3:0.077:52 | |
| chr2 175244928 . G T . t_lod_fstar ClippingRankSum=0;DP=648;ECNT=1;FS=3.211;HCNT=35;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=40.23;ReadPosRankSum=1.117;TLOD=4.99;ANN=T|splice_donor_variant&intron_variant|HIGH|CIR1|ENSG00000138433|transcript|ENST00000342016|protein_coding|6/9|c.366+2C>A||||||,T|splice_donor_variant&intron_variant|HIGH|CIR1|ENSG00000138433|transcript|ENST00000362053|protein_coding|6/10|c.366+2C>A||||||,T|splice_donor_variant&intron_variant|HIGH|CIR1|ENSG00000138433|transcript|ENST00000377973|protein_coding|2/3|c.78+2C>A||||||WARNING_TRANSCRIPT_NO_START_CODON,T|splice_donor_variant&intron_variant|HIGH|CIR1|ENSG00000138433|transcript|ENST00000461454|retained_intron|6/6|n.450+2C>A||||||;LOF=(CIR1|ENSG00000138433|6|0.50) GT:AD:AF:DP 0/1:439,5:0.014:444 0/0:204,0:0:204 | |
| chr2 178994066 . G T . t_lod_fstar ClippingRankSum=0;DP=50;ECNT=1;FS=2.413;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.31;ReadPosRankSum=-0.688;TLOD=4.13;ANN=T|intron_variant|MODIFIER|RBM45|ENSG00000155636|transcript|ENST00000286070|protein_coding|9/9|c.*9-58G>T||||||,T|intron_variant|MODIFIER|RBM45|ENSG00000155636|transcript|ENST00000424000|retained_intron|8/8|n.1733-58G>T||||||,T|intron_variant|MODIFIER|RBM45|ENSG00000155636|transcript|ENST00000455903|protein_coding|3/3|c.*8+3155G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|RBM45|ENSG00000155636|transcript|ENST00000424099|protein_coding|2/2|c.*9-58G>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|intron_variant|MODIFIER|RBM45|ENSG00000155636|transcript|ENST00000464647|processed_transcript|1/2|n.46+3155G>T|||||| GT:AD:AF:DP 0/1:31,4:0.08:35 0/0:15,0:0:15 | |
| chr2 179323420 . GCT G . t_lod_fstar ClippingRankSum=0;DP=184;ECNT=1;FS=1.273;HCNT=30;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.33;ReadPosRankSum=-1.185;TLOD=4.77;ANN=G|downstream_gene_variant|MODIFIER|AC009948.7|ENSG00000238082|transcript|ENST00000437039|processed_pseudogene||n.*3266_*3267delCT|||||3266|,G|downstream_gene_variant|MODIFIER|FKBP7|ENSG00000079150|transcript|ENST00000424785|protein_coding||c.*7075_*7076delAG|||||4970|,G|downstream_gene_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000605419|processed_transcript||n.*67_*68delCT|||||67|,G|intron_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000375129|protein_coding|4/5|c.667+79_667+80delCT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000409117|protein_coding|5/6|c.667+79_667+80delCT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000437056|retained_intron|3/4|n.1537+79_1537+80delCT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000442710|protein_coding|3/4|c.391-1642_391-1641delCT||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DFNB59|ENSG00000204311|transcript|ENST00000444615|nonsense_mediated_decay|3/4|c.307+79_307+80delCT||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:112,5:0.034:117 0/0:40,4:0.065:44 | |
| chr2 179422267 . G C . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=80;ECNT=4;FS=14.485;HCNT=15;MAX_ED=8;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=-1.254;TLOD=8.66;ANN=C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|329/363|c.87722C>G|p.Pro29241Arg|87947/109224|87722/107976|29241/35991||,C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|278/312|c.80018C>G|p.Pro26673Arg|80241/101518|80018/100272|26673/33423||,C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|158/192|c.61103C>G|p.Pro20368Arg|61328/82605|61103/81357|20368/27118||,C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|158/192|c.60902C>G|p.Pro20301Arg|61127/82404|60902/81156|20301/27051||,C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|157/191|c.60527C>G|p.Pro20176Arg|60752/82029|60527/80781|20176/26926||,C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|279/313|c.82799C>G|p.Pro27600Arg|83024/104301|82799/103053|27600/34350||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000419746|antisense|7/16|n.2043+15179G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000456053|antisense|1/6|n.414-13760G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586707|antisense|1/2|n.346-26173G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592600|antisense|1/1|n.346-27033G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000591332|antisense|2/2|n.442+21712G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592750|antisense|1/3|n.345+33904G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|2/3|n.433+19849G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.198+33904G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586831|antisense|2/4|n.214+15179G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592689|antisense|5/5|n.462+15179G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586452|antisense|1/6|n.75-13760G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590807|antisense|1/5|n.75-25984G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000438095|antisense|2/3|n.195-13760G>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590932|antisense|1/1|n.615+15179G>C|||||| GT:AD:AF:DP:PGT:PID 0/1:53,3:0.064:56:0|1:179422267_G_C 0/0:24,0:0:24:0|1:179422267_G_C | |
| chr2 179422268 . G T . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=81;ECNT=4;FS=14.649;HCNT=15;MAX_ED=8;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=-1.138;TLOD=8.68;ANN=T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|329/363|c.87721C>A|p.Pro29241Thr|87946/109224|87721/107976|29241/35991||,T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|278/312|c.80017C>A|p.Pro26673Thr|80240/101518|80017/100272|26673/33423||,T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|158/192|c.61102C>A|p.Pro20368Thr|61327/82605|61102/81357|20368/27118||,T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|158/192|c.60901C>A|p.Pro20301Thr|61126/82404|60901/81156|20301/27051||,T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|157/191|c.60526C>A|p.Pro20176Thr|60751/82029|60526/80781|20176/26926||,T|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|279/313|c.82798C>A|p.Pro27600Thr|83023/104301|82798/103053|27600/34350||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000419746|antisense|7/16|n.2043+15180G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000456053|antisense|1/6|n.414-13759G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586707|antisense|1/2|n.346-26172G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592600|antisense|1/1|n.346-27032G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000591332|antisense|2/2|n.442+21713G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592750|antisense|1/3|n.345+33905G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|2/3|n.433+19850G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.198+33905G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586831|antisense|2/4|n.214+15180G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592689|antisense|5/5|n.462+15180G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586452|antisense|1/6|n.75-13759G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590807|antisense|1/5|n.75-25983G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000438095|antisense|2/3|n.195-13759G>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590932|antisense|1/1|n.615+15180G>T|||||| GT:AD:AF:DP:PGT:PID 0/1:54,3:0.065:57:0|1:179422267_G_C 0/0:24,0:0:24:0|1:179422267_G_C | |
| chr2 179422269 . T A . clustered_events;homologous_mapping_event ClippingRankSum=0;DP=83;ECNT=4;FS=14.479;HCNT=15;MAX_ED=8;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.72;ReadPosRankSum=-0.891;TLOD=8.71;ANN=A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|329/363|c.87720A>T|p.Pro29240Pro|87945/109224|87720/107976|29240/35991||,A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|278/312|c.80016A>T|p.Pro26672Pro|80239/101518|80016/100272|26672/33423||,A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|158/192|c.61101A>T|p.Pro20367Pro|61326/82605|61101/81357|20367/27118||,A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|158/192|c.60900A>T|p.Pro20300Pro|61125/82404|60900/81156|20300/27051||,A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|157/191|c.60525A>T|p.Pro20175Pro|60750/82029|60525/80781|20175/26926||,A|synonymous_variant|LOW|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|279/313|c.82797A>T|p.Pro27599Pro|83022/104301|82797/103053|27599/34350||,A|sequence_feature|LOW|TTN|ENSG00000155657|domain:Fibronectin_type-III_101|ENST00000342992|protein_coding|278/312|c.80016A>T||||||,A|sequence_feature|LOW|TTN|ENSG00000155657|domain:Fibronectin_type-III_101|ENST00000359218|protein_coding|158/192|c.60900A>T||||||,A|sequence_feature|LOW|TTN|ENSG00000155657|domain:Fibronectin_type-III_101|ENST00000460472|protein_coding|157/191|c.60525A>T||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000419746|antisense|7/16|n.2043+15181T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000456053|antisense|1/6|n.414-13758T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586707|antisense|1/2|n.346-26171T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592600|antisense|1/1|n.346-27031T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000591332|antisense|2/2|n.442+21714T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592750|antisense|1/3|n.345+33906T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|2/3|n.433+19851T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.198+33906T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586831|antisense|2/4|n.214+15181T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592689|antisense|5/5|n.462+15181T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586452|antisense|1/6|n.75-13758T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590807|antisense|1/5|n.75-25982T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000438095|antisense|2/3|n.195-13758T>A||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590932|antisense|1/1|n.615+15181T>A|||||| GT:AD:AF:DP:PGT:PID 0/1:56,3:0.067:59:0|1:179422267_G_C 0/0:24,0:0:24:0|1:179422267_G_C | |
| chr2 179422275 . AGGTGTTG A . clustered_events;homologous_mapping_event;t_lod_fstar ClippingRankSum=0;DP=91;ECNT=4;FS=13.476;HCNT=15;MAX_ED=8;MIN_ED=1;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.32;ReadPosRankSum=-0.353;TLOD=5.34;ANN=A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|329/363|c.87707_87713delCAACACC|p.Thr29236fs|87938/109224|87707/107976|29236/35991||,A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|278/312|c.80003_80009delCAACACC|p.Thr26668fs|80232/101518|80003/100272|26668/33423||,A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|158/192|c.61088_61094delCAACACC|p.Thr20363fs|61319/82605|61088/81357|20363/27118||,A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|158/192|c.60887_60893delCAACACC|p.Thr20296fs|61118/82404|60887/81156|20296/27051||,A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|157/191|c.60512_60518delCAACACC|p.Thr20171fs|60743/82029|60512/80781|20171/26926||,A|frameshift_variant&splice_region_variant|HIGH|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|279/313|c.82784_82790delCAACACC|p.Thr27595fs|83015/104301|82784/103053|27595/34350||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000419746|antisense|7/16|n.2043+15188_2043+15194delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000456053|antisense|1/6|n.414-13751_414-13745delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586707|antisense|1/2|n.346-26164_346-26158delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592600|antisense|1/1|n.346-27024_346-27018delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000591332|antisense|2/2|n.442+21721_442+21727delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592750|antisense|1/3|n.345+33913_345+33919delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|2/3|n.433+19858_433+19864delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.198+33913_198+33919delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586831|antisense|2/4|n.214+15188_214+15194delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592689|antisense|5/5|n.462+15188_462+15194delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000586452|antisense|1/6|n.75-13751_75-13745delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590807|antisense|1/5|n.75-25975_75-25969delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000438095|antisense|2/3|n.195-13751_195-13745delGGTGTTG||||||,A|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000590932|antisense|1/1|n.615+15188_615+15194delGGTGTTG||||||;LOF=(TTN|ENSG00000155657|15|0.40) GT:AD:AF:DP:PGT:PID 0/1:61,3:0.039:64:0|1:179422267_G_C 0/0:27,0:0:27:0|1:179422267_G_C | |
| chr2 179527824 . T C . PASS ClippingRankSum=0;DP=402;ECNT=1;FS=23.531;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=43.27;MQ0=53;MQRankSum=-2.723;NLOD=27.93;ReadPosRankSum=-0.884;TLOD=16.24;ANN=C|downstream_gene_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000425332|protein_coding||c.*530A>G|||||530|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|173/362|c.36701-42A>G||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|3/3|n.520-50657T>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.199-97843T>C||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|152/311|c.31484-42A>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|47/191|c.13859-20780A>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|47/191|c.13658-20780A>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|46/190|c.13283-20780A>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|153/312|c.34265-4303A>G||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589830|antisense|2/2|n.211+26399T>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589487|antisense|2/6|n.319-12005T>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000431752|antisense|1/1|n.124+26399T>C||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000414766|protein_coding|26/31|c.2440+10536A>G||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:175,11:0.077:186 0/0:133,5:0.046:138 | |
| chr2 179528038 . A C . PASS ClippingRankSum=0;DP=364;ECNT=1;FS=0.844;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=48.49;MQ0=29;MQRankSum=1.432;NLOD=9.74;ReadPosRankSum=-0.82;TLOD=9.62;ANN=C|missense_variant|MODERATE|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|173/363|c.36655T>G|p.Leu12219Val|36880/109224|36655/107976|12219/35991||,C|downstream_gene_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000425332|protein_coding||c.*316T>G|||||316|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|3/3|n.520-50443A>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.199-97629A>C||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|152/311|c.31484-256T>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|47/191|c.13859-20994T>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|47/191|c.13658-20994T>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|46/190|c.13283-20994T>G||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|153/312|c.34265-4517T>G||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589830|antisense|2/2|n.211+26613A>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589487|antisense|2/6|n.319-11791A>C||||||,C|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000431752|antisense|1/1|n.124+26613A>C||||||,C|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000414766|protein_coding|26/31|c.2440+10322T>G||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:158,6:0.051:164 0/0:147,15:0.126:162 | |
| chr2 179534224 . C T . PASS ClippingRankSum=0;DP=330;ECNT=1;FS=0;HCNT=26;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=24.65;ReadPosRankSum=0.496;TLOD=44.58;ANN=T|upstream_gene_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000425332|protein_coding||c.-2192G>A|||||2190|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000448510|protein_coding||c.*128G>A|||||128|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000589042|protein_coding|158/362|c.35471-50G>A||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000592630|antisense|3/3|n.520-44257C>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000585451|antisense|1/4|n.199-91443C>T||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342992|protein_coding|152/311|c.31483+721G>A||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000342175|protein_coding|47/191|c.13859-27180G>A||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000359218|protein_coding|47/191|c.13658-27180G>A||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000460472|protein_coding|46/190|c.13283-27180G>A||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000591111|protein_coding|153/312|c.34264+721G>A||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589830|antisense|2/2|n.211+32799C>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000589487|antisense|2/6|n.319-5605C>T||||||,T|intron_variant|MODIFIER|TTN-AS1|ENSG00000237298|transcript|ENST00000431752|antisense|1/1|n.124+32799C>T||||||,T|intron_variant|MODIFIER|TTN|ENSG00000155657|transcript|ENST00000414766|protein_coding|26/31|c.2440+4136G>A||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:192,30:0.131:222 0/0:108,0:0:108 | |
| chr2 180310271 . C T . PASS ClippingRankSum=0;DP=135;ECNT=1;FS=0.753;HCNT=64;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.73;ReadPosRankSum=-1.042;TLOD=98.43;ANN=T|splice_region_variant&intron_variant|LOW|ZNF385B|ENSG00000144331|transcript|ENST00000410066|protein_coding|8/9|c.1095+6G>A||||||,T|splice_region_variant&intron_variant|LOW|ZNF385B|ENSG00000144331|transcript|ENST00000466398|processed_transcript|10/12|n.1369+6G>A||||||,T|splice_region_variant&intron_variant|LOW|ZNF385B|ENSG00000144331|transcript|ENST00000336917|protein_coding|6/7|c.789+6G>A||||||,T|splice_region_variant&intron_variant|LOW|ZNF385B|ENSG00000144331|transcript|ENST00000409343|protein_coding|6/7|c.867+6G>A||||||,T|splice_region_variant&intron_variant|LOW|ZNF385B|ENSG00000144331|transcript|ENST00000409692|protein_coding|7/8|c.789+6G>A||||||,T|downstream_gene_variant|MODIFIER|ZNF385B|ENSG00000144331|transcript|ENST00000457304|protein_coding||c.*6G>A|||||6|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ZNF385B|ENSG00000144331|transcript|ENST00000469551|processed_transcript||n.*64G>A|||||64|,T|downstream_gene_variant|MODIFIER|ZNF385B|ENSG00000144331|transcript|ENST00000475539|processed_transcript||n.*1090G>A|||||1090| GT:AD:AF:DP 0/1:41,44:0.515:85 0/0:50,0:0:50 | |
| chr2 182403896 . ATCC A . t_lod_fstar ClippingRankSum=0;DP=500;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=-0.138;NLOD=19.53;ReadPosRankSum=-0.117;TLOD=4.13;ANN=A|disruptive_inframe_deletion|MODERATE|CERKL|ENSG00000188452|transcript|ENST00000339098|protein_coding|13/14|c.1536_1538delGGA|p.Glu512del|1538/1677|1536/1677|512/558||,A|disruptive_inframe_deletion|MODERATE|CERKL|ENSG00000188452|transcript|ENST00000410087|protein_coding|12/13|c.1458_1460delGGA|p.Glu486del|1561/3208|1458/1599|486/532||,A|disruptive_inframe_deletion|MODERATE|CERKL|ENSG00000188452|transcript|ENST00000409440|protein_coding|12/13|c.1404_1406delGGA|p.Glu468del|1507/2425|1404/1545|468/514||,A|disruptive_inframe_deletion|MODERATE|CERKL|ENSG00000188452|transcript|ENST00000374969|protein_coding|9/10|c.1119_1121delGGA|p.Glu373del|1121/1330|1119/1260|373/419||,A|disruptive_inframe_deletion|MODERATE|CERKL|ENSG00000188452|transcript|ENST00000374970|protein_coding|10/11|c.1251_1253delGGA|p.Glu417del|1253/1392|1251/1392|417/463||,A|3_prime_UTR_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000374967|nonsense_mediated_decay|11/12|c.*740_*742delGGA|||||19496|,A|3_prime_UTR_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000452174|nonsense_mediated_decay|10/11|c.*740_*742delGGA|||||19496|,A|3_prime_UTR_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000421817|nonsense_mediated_decay|9/10|c.*714_*716delGGA|||||19496|,A|downstream_gene_variant|MODIFIER|ITGA4|ENSG00000115232|transcript|ENST00000397033|protein_coding||c.*3643_*3645delTCC|||||2983|,A|non_coding_transcript_exon_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000494398|retained_intron|10/11|n.2250_2252delGGA|||||| GT:AD:AF:DP 0/1:286,2:0.009852:288 0/0:142,3:0.021:145 | |
| chr2 182542987 . G T . t_lod_fstar ClippingRankSum=0;DP=74;ECNT=1;FS=0;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.82;ReadPosRankSum=2.045;TLOD=4.03;ANN=T|missense_variant|MODERATE|NEUROD1|ENSG00000162992|transcript|ENST00000295108|protein_coding|2/2|c.601C>A|p.Gln201Lys|1059/2852|601/1071|201/356||,T|upstream_gene_variant|MODIFIER|AC013733.3|ENSG00000234595|transcript|ENST00000440371|antisense||n.-4853G>T|||||4853|,T|intron_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000479558|processed_transcript|1/10|n.236+2170C>A||||||,T|intron_variant|MODIFIER|CERKL|ENSG00000188452|transcript|ENST00000497337|processed_transcript|1/2|n.212+2170C>A||||||,T|intron_variant|MODIFIER|NEUROD1|ENSG00000162992|transcript|ENST00000496876|processed_transcript|1/1|n.118+2170C>A|||||| GT:AD:AF:DP 0/1:34,3:0.071:37 0/0:37,0:0:37 | |
| chr2 183799604 . G T . t_lod_fstar ClippingRankSum=0;DP=342;ECNT=1;FS=1.994;HCNT=17;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=23.77;ReadPosRankSum=-0.272;TLOD=4.07;ANN=T|intron_variant|MODIFIER|NCKAP1|ENSG00000061676|transcript|ENST00000360982|protein_coding|26/31|c.2797-44C>A||||||,T|intron_variant|MODIFIER|NCKAP1|ENSG00000061676|transcript|ENST00000361354|protein_coding|25/30|c.2779-44C>A||||||,T|intron_variant|MODIFIER|NCKAP1|ENSG00000061676|transcript|ENST00000478449|processed_transcript|3/6|n.314-44C>A||||||,T|intron_variant|MODIFIER|NCKAP1|ENSG00000061676|transcript|ENST00000471640|processed_transcript|2/3|n.162-44C>A||||||,T|intron_variant|MODIFIER|NCKAP1|ENSG00000061676|transcript|ENST00000492058|retained_intron|1/1|n.212-44C>A|||||| GT:AD:AF:DP 0/1:231,5:0.023:236 0/0:106,0:0:106 | |
| chr2 185463815 . CCT C . PASS ClippingRankSum=0;DP=266;ECNT=1;FS=1.454;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=60.04;MQ0=0;MQRankSum=4.595;NLOD=5.69;ReadPosRankSum=-2.381;TLOD=6.42;ANN=C|intron_variant|MODIFIER|ZNF804A|ENSG00000170396|transcript|ENST00000302277|protein_coding|1/3|c.111+32_111+33delTC||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:109,5:0.051:114 0/0:79,4:0.057:83 | |
| chr2 185800880 . G T . t_lod_fstar ClippingRankSum=0;DP=159;ECNT=1;FS=4.498;HCNT=40;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.53;ReadPosRankSum=-0.154;TLOD=4.87;ANN=T|missense_variant|MODERATE|ZNF804A|ENSG00000170396|transcript|ENST00000302277|protein_coding|4/4|c.757G>T|p.Val253Phe|1351/4690|757/3630|253/1209|| GT:AD:AF:DP 0/1:109,4:0.037:113 0/0:46,0:0:46 | |
| chr2 188361690 . G T . t_lod_fstar ClippingRankSum=0;DP=286;ECNT=1;FS=0;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.80;ReadPosRankSum=0.661;TLOD=4.65;ANN=T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000233156|protein_coding|3/8|c.237C>A|p.Cys79*|532/3913|237/915|79/304||,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000392365|protein_coding|3/8|c.237C>A|p.Cys79*|265/3649|237/915|79/304||,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000426055|protein_coding|3/8|c.237C>A|p.Cys79*|532/1161|237/866|79/287||WARNING_TRANSCRIPT_INCOMPLETE,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000435414|protein_coding|3/6|c.237C>A|p.Cys79*|277/687|237/647|79/214||WARNING_TRANSCRIPT_INCOMPLETE,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000409676|protein_coding|4/8|c.237C>A|p.Cys79*|502/1119|237/756|79/251||,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000339091|protein_coding|3/7|c.237C>A|p.Cys79*|478/1088|237/756|79/251||,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000437725|protein_coding|4/4|c.237C>A|p.Cys79*|463/545|237/319|79/105||WARNING_TRANSCRIPT_INCOMPLETE,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000421427|protein_coding|5/5|c.237C>A|p.Cys79*|722/804|237/319|79/105||WARNING_TRANSCRIPT_INCOMPLETE,T|stop_gained|HIGH|TFPI|ENSG00000003436|transcript|ENST00000453013|protein_coding|4/4|c.237C>A|p.Cys79*|654/733|237/316|79/104||WARNING_TRANSCRIPT_INCOMPLETE,T|sequence_feature|MODERATE|TFPI|ENSG00000003436|disulfide-bond:match_to_sequence_model_evidence_used_in_manual_assertion|ENST00000392365|protein_coding|3/8|c.237C>A||||||,T|sequence_feature|MODERATE|TFPI|ENSG00000003436|disulfide-bond:match_to_sequence_model_evidence_used_in_manual_assertion|ENST00000409676|protein_coding|4/8|c.237C>A||||||,T|downstream_gene_variant|MODIFIER|TFPI|ENSG00000003436|transcript|ENST00000417013|protein_coding||c.*9C>A|||||9|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|TFPI|ENSG00000003436|transcript|ENST00000420747|protein_coding||c.*53C>A|||||53|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|AC007319.1|ENSG00000224063|transcript|ENST00000412276|antisense|2/6|n.190-2543G>T||||||,T|intron_variant|MODIFIER|AC007319.1|ENSG00000224063|transcript|ENST00000453517|antisense|2/3|n.244-2543G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|TFPI|ENSG00000003436|transcript|ENST00000481132|retained_intron|3/7|n.6484C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|TFPI|ENSG00000003436|transcript|ENST00000481389|retained_intron|1/4|n.14C>A||||||;LOF=(TFPI|ENSG00000003436|13|0.46);NMD=(TFPI|ENSG00000003436|13|0.46) GT:AD:AF:DP 0/1:188,4:0.023:192 0/0:94,0:0:94 | |
| chr2 190425524 . G T . t_lod_fstar ClippingRankSum=0;DP=245;ECNT=1;FS=2.487;HCNT=41;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=17.15;ReadPosRankSum=0.377;TLOD=4.16;ANN=T|3_prime_UTR_variant|MODIFIER|SLC40A1|ENSG00000138449|transcript|ENST00000261024|protein_coding|8/8|c.*1080C>A|||||1080|,T|downstream_gene_variant|MODIFIER|SLC40A1|ENSG00000138449|transcript|ENST00000427241|protein_coding||c.*4715C>A|||||4715|WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:162,3:0.023:165 0/0:80,0:0:80 | |
| chr2 190742010 . C T . PASS ClippingRankSum=0;DP=195;ECNT=1;FS=2.688;HCNT=50;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=12.93;ReadPosRankSum=-0.358;TLOD=114.86;ANN=T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000441310|protein_coding|13/13|c.2647C>T|p.Arg883Cys|2880/3225|2647/2799|883/932||,T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000418224|protein_coding|12/12|c.2119C>T|p.Arg707Cys|2669/3012|2119/2271|707/756||,T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000409823|protein_coding|12/12|c.2530C>T|p.Arg844Cys|2643/2795|2530/2682|844/893||,T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000447232|protein_coding|12/12|c.2161C>T|p.Arg721Cys|2231/2576|2161/2313|721/770||,T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000432292|protein_coding|11/11|c.2119C>T|p.Arg707Cys|2410/2659|2119/2271|707/756||,T|missense_variant|MODERATE|PMS1|ENSG00000064933|transcript|ENST00000409593|protein_coding|7/7|c.1516C>T|p.Arg506Cys|1516/1668|1516/1668|506/555||,T|3_prime_UTR_variant|MODIFIER|PMS1|ENSG00000064933|transcript|ENST00000342075|nonsense_mediated_decay|12/12|c.*2217C>T|||||59256|,T|3_prime_UTR_variant|MODIFIER|PMS1|ENSG00000064933|transcript|ENST00000450931|nonsense_mediated_decay|13/13|c.*296C>T|||||9477|,T|upstream_gene_variant|MODIFIER|C2orf88|ENSG00000187699|transcript|ENST00000478197|processed_transcript||n.-2325C>T|||||2325|,T|upstream_gene_variant|MODIFIER|C2orf88|ENSG00000187699|transcript|ENST00000495546|processed_transcript||n.-2343C>T|||||2343|,T|downstream_gene_variant|MODIFIER|PMS1|ENSG00000064933|transcript|ENST00000424059|processed_transcript||n.*3756C>T|||||3756|,T|downstream_gene_variant|MODIFIER|PMS1|ENSG00000064933|transcript|ENST00000452382|protein_coding||c.*3628C>T|||||3628|WARNING_TRANSCRIPT_NO_STOP_CODON GT:AD:AF:DP 0/1:72,66:0.473:138 0/0:57,0:0:57 | |
| chr2 190788451 . ACCT A . t_lod_fstar ClippingRankSum=0;DP=201;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.15;ReadPosRankSum=0.322;TLOD=4.91;ANN=A|intron_variant|MODIFIER|C2orf88|ENSG00000187699|transcript|ENST00000478197|processed_transcript|1/1|n.219+43911_219+43913delCCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|C2orf88|ENSG00000187699|transcript|ENST00000495546|processed_transcript|1/2|n.201+43911_201+43913delCCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|HNRNPCP2|ENSG00000204253|transcript|ENST00000342709|processed_pseudogene|1/2|n.117+286_118-286delCCT||||||INFO_REALIGN_3_PRIME,A|non_coding_transcript_exon_variant|MODIFIER|HNRNPCP2|ENSG00000204253|transcript|ENST00000399515|processed_pseudogene|1/1|n.403_405delCCT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:112,3:0.024:115 0/0:68,1:0.019:69 | |
| chr2 196571396 . G A . PASS ClippingRankSum=0;DP=156;ECNT=1;FS=2.146;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.48;ReadPosRankSum=0;TLOD=103.12;ANN=A|missense_variant|MODERATE|SLC39A10|ENSG00000196950|transcript|ENST00000359634|protein_coding|4/10|c.1273G>A|p.Val425Met|1438/5322|1273/2496|425/831||,A|missense_variant|MODERATE|SLC39A10|ENSG00000196950|transcript|ENST00000409086|protein_coding|4/10|c.1273G>A|p.Val425Met|1548/5432|1273/2496|425/831||,A|5_prime_UTR_premature_start_codon_gain_variant|LOW|SLC39A10|ENSG00000196950|transcript|ENST00000541054|protein_coding|5/11|c.-78G>A||||||,A|5_prime_UTR_variant|MODIFIER|SLC39A10|ENSG00000196950|transcript|ENST00000541054|protein_coding|5/11|c.-78G>A|||||78|,A|3_prime_UTR_variant|MODIFIER|SLC39A10|ENSG00000196950|transcript|ENST00000444421|nonsense_mediated_decay|5/5|c.*309G>A|||||25666|,A|3_prime_UTR_variant|MODIFIER|SLC39A10|ENSG00000196950|transcript|ENST00000430412|nonsense_mediated_decay|5/11|c.*309G>A|||||25666|,A|non_coding_transcript_exon_variant|MODIFIER|SLC39A10|ENSG00000196950|transcript|ENST00000465851|retained_intron|3/6|n.839G>A|||||| GT:AD:AF:DP 0/1:55,53:0.494:108 0/0:48,0:0:48 | |
| chr2 196822102 . C T . t_lod_fstar ClippingRankSum=0;DP=156;ECNT=1;FS=0;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.68;ReadPosRankSum=-0.466;TLOD=4.48;ANN=T|stop_gained|HIGH|DNAH7|ENSG00000118997|transcript|ENST00000312428|protein_coding|19/65|c.2961G>A|p.Trp987*|3062/12394|2961/12075|987/4024||;LOF=(DNAH7|ENSG00000118997|8|0.13);NMD=(DNAH7|ENSG00000118997|8|0.13) GT:AD:AF:DP 0/1:109,5:0.037:114 0/0:41,0:0:41 | |
| chr2 197943382 . ATG A . PASS ClippingRankSum=0;DP=115;ECNT=1;FS=0;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.72;ReadPosRankSum=0.973;TLOD=10.92;ANN=A|frameshift_variant|HIGH|ANKRD44|ENSG00000065413|transcript|ENST00000409153|protein_coding|16/16|c.1693_1694delCA|p.His565fs|1877/2724|1693/1740|565/579||,A|frameshift_variant|HIGH|ANKRD44|ENSG00000065413|transcript|ENST00000539527|protein_coding|15/15|c.1477_1478delCA|p.His493fs|1808/1994|1477/1524|493/507||,A|downstream_gene_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000477852|processed_transcript||n.*3031_*3032delCA|||||3032|,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000282272|protein_coding|15/26|c.1626+43_1626+44delCA||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000424317|protein_coding|10/21|c.1095+43_1095+44delCA||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000337207|protein_coding|15/24|c.1575+43_1575+44delCA||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000450567|protein_coding|15/24|c.1575+43_1575+44delCA||||||,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000328737|protein_coding|16/25|c.1575+43_1575+44delCA||||||,A|intron_variant|MODIFIER|ANKRD44|ENSG00000065413|transcript|ENST00000422886|protein_coding|7/8|c.675+43_675+44delCA||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:55,11:0.12:66 0/0:38,2:0.067:40 | |
| chr2 202345075 . C T . PASS ClippingRankSum=0;DP=178;ECNT=1;FS=13.135;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=58.29;MQ0=2;MQRankSum=-7.826;NLOD=8.97;ReadPosRankSum=-2.949;TLOD=8.25;ANN=T|3_prime_UTR_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000194530|protein_coding|12/12|c.*177C>T|||||177|,T|3_prime_UTR_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000392249|protein_coding|12/12|c.*324C>T|||||324|,T|3_prime_UTR_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000415688|protein_coding|4/4|c.*177C>T|||||177|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000458269|protein_coding||c.*2239C>T|||||2239|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000484098|retained_intron||n.*2627C>T|||||2627|,T|downstream_gene_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000498648|retained_intron||n.*2161C>T|||||2161|,T|downstream_gene_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000468123|retained_intron||n.*1785C>T|||||1785|,T|downstream_gene_variant|MODIFIER|STRADB|ENSG00000082146|transcript|ENST00000466770|retained_intron||n.*4C>T|||||4| GT:AD:AF:DP 0/1:124,6:0.067:130 0/0:44,1:0.032:45 | |
| chr2 202899419 . G T . t_lod_fstar ClippingRankSum=0;DP=35;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=-0.26;TLOD=4.59;ANN=T|missense_variant|MODERATE|FZD7|ENSG00000155760|transcript|ENST00000286201|protein_coding|1/1|c.49G>T|p.Ala17Ser|110/3851|49/1725|17/574||,T|upstream_gene_variant|MODIFIER|RP11-107N15.1|ENSG00000273209|transcript|ENST00000608741|lincRNA||n.-1159C>A|||||1159| GT:AD:AF:DP 0/1:16,2:0.118:18 0/0:16,0:0:16 | |
| chr2 203942441 . CTTAT C . PASS ClippingRankSum=0;DP=477;ECNT=1;FS=5.018;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=24.61;ReadPosRankSum=0.69;TLOD=6.80;ANN=C|upstream_gene_variant|MODIFIER|AC023271.2|ENSG00000225124|transcript|ENST00000413895|processed_pseudogene||n.-2580_-2577delATAA|||||2577|,C|intron_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000449802|protein_coding|7/54|c.599-12_599-9delTATT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000497505|retained_intron|7/10|n.932-12_932-9delTATT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:283,4:0.016:287 0/0:113,0:0:113 | |
| chr2 204036703 . C T . t_lod_fstar ClippingRankSum=0;DP=180;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.93;ReadPosRankSum=1.059;TLOD=4.53;ANN=T|missense_variant|MODERATE|NBEAL1|ENSG00000144426|transcript|ENST00000449802|protein_coding|39/55|c.6068C>T|p.Thr2023Ile|6401/10938|6068/8085|2023/2694||,T|intron_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000414576|protein_coding|2/17|c.157-749C>T||||||WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:120,5:0.036:125 0/0:54,0:0:54 | |
| chr2 204055840 . T C . germline_risk ClippingRankSum=0;DP=170;ECNT=1;FS=3.298;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=48.97;MQ0=4;MQRankSum=-2.088;NLOD=1.47;ReadPosRankSum=-1.661;TLOD=11.09;ANN=C|intron_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000449802|protein_coding|45/54|c.6834+728T>C||||||,C|intron_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000414576|protein_coding|8/17|c.879+728T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,C|non_coding_transcript_exon_variant|MODIFIER|AC011737.2|ENSG00000204196|transcript|ENST00000431098|processed_pseudogene|1/1|n.338T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NBEAL1|ENSG00000144426|transcript|ENST00000460355|retained_intron|3/3|n.3377T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|AC011737.2|ENSG00000204196|transcript|ENST00000314394|pseudogene|2/2|n.239T>C|||||| GT:AD:AF:DP 0/1:110,6:0.077:116 0/0:39,2:0.069:41 | |
| chr2 206327362 . G T . t_lod_fstar ClippingRankSum=0;DP=214;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=14.10;ReadPosRankSum=1.233;TLOD=4.69;ANN=T|intron_variant|MODIFIER|PARD3B|ENSG00000116117|transcript|ENST00000406610|protein_coding|20/22|c.3044+21966G>T||||||,T|intron_variant|MODIFIER|PARD3B|ENSG00000116117|transcript|ENST00000349953|protein_coding|19/21|c.2742-37258G>T||||||,T|intron_variant|MODIFIER|PARD3B|ENSG00000116117|transcript|ENST00000351153|protein_coding|19/21|c.2837+21966G>T||||||,T|intron_variant|MODIFIER|PARD3B|ENSG00000116117|transcript|ENST00000358768|protein_coding|19/21|c.2858+21966G>T|||||| GT:AD:AF:DP 0/1:141,4:0.03:145 0/0:68,0:0:68 | |
| chr2 206869416 . C T . t_lod_fstar ClippingRankSum=0;DP=33;ECNT=1;FS=0;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.31;ReadPosRankSum=1.53;TLOD=4.17;ANN=T|synonymous_variant|LOW|INO80D|ENSG00000114933|transcript|ENST00000403263|protein_coding|11/11|c.2760G>A|p.Thr920Thr|3165/14136|2760/3084|920/1027||,T|downstream_gene_variant|MODIFIER|AC007679.3|ENSG00000225610|transcript|ENST00000422116|antisense||n.*3834C>T|||||3834|,T|downstream_gene_variant|MODIFIER|Vault|ENSG00000252485|transcript|ENST00000516676|misc_RNA||n.*3188G>A|||||3188| GT:AD:AF:DP 0/1:17,4:0.143:21 0/0:12,0:0:12 | |
| chr2 208631298 . G T . t_lod_fstar ClippingRankSum=0;DP=224;ECNT=1;FS=4.296;HCNT=10;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.19;ReadPosRankSum=-0.702;TLOD=4.77;ANN=T|3_prime_UTR_variant|MODIFIER|FZD5|ENSG00000163251|transcript|ENST00000295417|protein_coding|2/2|c.*408C>A|||||408|,T|downstream_gene_variant|MODIFIER|CCNYL1|ENSG00000163249|transcript|ENST00000420321|protein_coding||c.*4893G>T|||||4735|WARNING_TRANSCRIPT_NO_START_CODON GT:AD:AF:DP 0/1:149,5:0.029:154 0/0:70,0:0:70 | |
| chr2 208728638 . AAT A . t_lod_fstar ClippingRankSum=0;DP=101;ECNT=1;FS=0;HCNT=9;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.13;ReadPosRankSum=-1.599;TLOD=5.81;ANN=A|downstream_gene_variant|MODIFIER|AC083900.1|ENSG00000225111|transcript|ENST00000421964|sense_intronic||n.*4666_*4667delAT|||||4667|,A|intron_variant|MODIFIER|PLEKHM3|ENSG00000178385|transcript|ENST00000427836|protein_coding|6/7|c.1951-2654_1951-2653delAT||||||,A|intron_variant|MODIFIER|PLEKHM3|ENSG00000178385|transcript|ENST00000447645|protein_coding|4/6|c.1204-2654_1204-2653delAT||||||WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|PLEKHM3|ENSG00000178385|transcript|ENST00000389247|protein_coding|6/7|c.1951-2654_1951-2653delAT|||||| GT:AD:AF:DP 0/1:49,4:0.12:53 0/0:29,0:0:29 | |
| chr2 209201528 . CAT C . PASS ClippingRankSum=0;DP=236;ECNT=1;FS=1.058;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.30;ReadPosRankSum=1.014;TLOD=10.64;ANN=C|downstream_gene_variant|MODIFIER|PIKFYVE|ENSG00000115020|transcript|ENST00000452564|protein_coding||c.*949_*950delAT|||||949|WARNING_TRANSCRIPT_NO_STOP_CODON,C|intron_variant|MODIFIER|PIKFYVE|ENSG00000115020|transcript|ENST00000264380|protein_coding|27/41|c.4521-21_4521-20delAT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|PIKFYVE|ENSG00000115020|transcript|ENST00000474721|processed_transcript|4/4|n.511-21_511-20delAT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:148,9:0.057:157 0/0:59,5:0.071:64 | |
| chr2 210384913 . T A . t_lod_fstar ClippingRankSum=0;DP=84;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=1.032;TLOD=4.53;ANN=A|intron_variant|MODIFIER|MAP2|ENSG00000078018|transcript|ENST00000199940|protein_coding|2/14|c.-172+12548T>A|||||| GT:AD:AF:DP 0/1:51,4:0.05:55 0/0:29,0:0:29 | |
| chr2 210838004 . TTC T . t_lod_fstar ClippingRankSum=0;DP=45;ECNT=1;FS=0;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.99;ReadPosRankSum=-1.734;TLOD=6.21;ANN=T|downstream_gene_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000489023|retained_intron||n.*2967_*2968delTC|||||2967|,T|intron_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000439458|protein_coding|55/63|c.8389+26_8389+27delCT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000272845|protein_coding|55/62|c.8374+26_8374+27delCT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000333907|protein_coding|6/9|c.967+26_967+27delCT||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000477924|processed_transcript|7/14|n.1137+26_1137+27delCT||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|UNC80|ENSG00000144406|transcript|ENST00000539183|protein_coding|6/9|c.727+26_727+27delCT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:18,4:0.2:22 0/0:16,0:0:16 | |
| chr2 210887344 . ATATG A . t_lod_fstar ClippingRankSum=0;DP=181;ECNT=1;FS=0;HCNT=30;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.92;ReadPosRankSum=2.108;TLOD=4.80;ANN=A|3_prime_UTR_variant|MODIFIER|KANSL1L|ENSG00000144445|transcript|ENST00000281772|protein_coding|15/15|c.*325_*328delCATA|||||325|,A|3_prime_UTR_variant|MODIFIER|KANSL1L|ENSG00000144445|transcript|ENST00000418791|protein_coding|14/14|c.*325_*328delCATA|||||325|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000359429|protein_coding||c.*2830_*2833delTATG|||||1045|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000436630|protein_coding||c.*2830_*2833delTATG|||||2521|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000408981|protein_coding||c.*2836_*2839delTATG|||||2836|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000454822|protein_coding||c.*2830_*2833delTATG|||||1395|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000429921|protein_coding||c.*2830_*2833delTATG|||||1045|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000540255|protein_coding||c.*2830_*2833delTATG|||||2111|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000438265|protein_coding||c.*4805_*4808delTATG|||||4805|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000429907|protein_coding||c.*4403_*4406delTATG|||||2681|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000445268|protein_coding||c.*2937_*2940delTATG|||||2886|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000452025|protein_coding||c.*2937_*2940delTATG|||||2855|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000438204|protein_coding||c.*2830_*2833delTATG|||||2660|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000411934|protein_coding||c.*2830_*2833delTATG|||||2660|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000435437|protein_coding||c.*2937_*2940delTATG|||||2660|,A|downstream_gene_variant|MODIFIER|RPE|ENSG00000197713|transcript|ENST00000354506|protein_coding||c.*2830_*2833delTATG|||||1078| GT:AD:AF:DP 0/1:135,4:0.021:139 0/0:34,0:0:34 | |
| chr2 211299162 . A AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT . t_lod_fstar ClippingRankSum=0;DP=151;ECNT=1;FS=0;HCNT=15;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.30;ReadPosRankSum=-0.523;TLOD=4.94;ANN=AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|3_prime_UTR_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000233714|protein_coding|10/10|c.*48_*49insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||48|,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|3_prime_UTR_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000443314|protein_coding|9/9|c.*48_*49insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||48|,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|3_prime_UTR_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000441020|protein_coding|10/10|c.*48_*49insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||48|,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|3_prime_UTR_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000450366|protein_coding|10/10|c.*48_*49insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||48|,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|downstream_gene_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000431941|protein_coding||c.*48_*49insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||48|,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|downstream_gene_variant|MODIFIER|LANCL1|ENSG00000115365|transcript|ENST00000412863|protein_coding||c.*82_*83insACGGAAGCACTTAGCTTGGGTTTGAATATACAGAAAGGGTCCTGCAACTCACTGCATGACCCTTTCTGTATAT|||||82|WARNING_TRANSCRIPT_INCOMPLETE,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|intron_variant|MODIFIER|AC007970.1|ENSG00000234281|transcript|ENST00000433296|antisense|4/4|n.456+5020_456+5021insACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGTATATACAGAAAGGGTCATGCAGTGAGTTGCAGG||||||INFO_REALIGN_3_PRIME,AATATACAGAAAGGGTCATGCAGTGAGTTGCAGGACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGT|intron_variant|MODIFIER|AC007970.1|ENSG00000234281|transcript|ENST00000420418|antisense|2/5|n.156+5020_156+5021insACCCTTTCTGTATATTCAAACCCAAGCTAAGTGCTTCCGTATATACAGAAAGGGTCATGCAGTGAGTTGCAGG||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:105,1:0.025:106 0/0:38,0:0:38 | |
| chr2 212240977 . C CA . PASS ClippingRankSum=0;DP=383;ECNT=1;FS=1.417;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=25.81;ReadPosRankSum=0.145;TLOD=133.52;ANN=CA|3_prime_UTR_variant|MODIFIER|ERBB4|ENSG00000178568|transcript|ENST00000342788|protein_coding|28/28|c.*7362dupT|||||7362|,CA|3_prime_UTR_variant|MODIFIER|ERBB4|ENSG00000178568|transcript|ENST00000436443|protein_coding|27/27|c.*7362dupT|||||7362| GT:AD:AF:DP 0/1:147,106:0.414:253 0/0:123,0:0:123 | |
| chr2 213628400 . A T . t_lod_fstar ClippingRankSum=0;DP=166;ECNT=1;FS=5.278;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=57.4;MQ0=2;MQRankSum=0.273;NLOD=9.58;ReadPosRankSum=0.813;TLOD=5.78;ANN=T|upstream_gene_variant|MODIFIER|AC093865.1|ENSG00000221388|transcript|ENST00000408461|miRNA||n.-1T>A|||||1|,T|intron_variant|MODIFIER|AC079610.1|ENSG00000273118|transcript|ENST00000415387|sense_overlapping|4/4|n.381+129009T>A|||||| GT:AD:AF:DP 0/1:101,4:0.041:105 0/0:36,0:0:36 | |
| chr2 213864846 . G C . t_lod_fstar ClippingRankSum=0;DP=99;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.02;ReadPosRankSum=0.195;TLOD=4.06;ANN=C|3_prime_UTR_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000457361|protein_coding|8/8|c.*7238C>G|||||7238|,C|intron_variant|MODIFIER|AC079610.1|ENSG00000273118|transcript|ENST00000415387|sense_overlapping|1/4|n.81+21343C>G|||||| GT:AD:AF:DP 0/1:69,1:0.04:70 0/0:28,0:0:28 | |
| chr2 214012403 . CAA C . PASS ClippingRankSum=0;DP=136;ECNT=1;FS=0;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.30;ReadPosRankSum=-0.947;TLOD=6.68;ANN=C|frameshift_variant|HIGH|IKZF2|ENSG00000030419|transcript|ENST00000442445|protein_coding|3/3|c.184_185delTT|p.Leu62fs|243/551|184/279|62/92||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000342002|protein_coding|3/7|c.157+27_157+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000457361|protein_coding|3/7|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000434687|protein_coding|4/8|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000374319|protein_coding|4/8|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000453575|nonsense_mediated_decay|2/7|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000374326|nonsense_mediated_decay|2/6|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000412444|nonsense_mediated_decay|2/8|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000439848|nonsense_mediated_decay|2/7|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000374327|protein_coding|2/4|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000413091|protein_coding|2/7|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000421754|protein_coding|2/5|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000431520|nonsense_mediated_decay|2/8|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000451136|protein_coding|2/5|c.139+27_139+28delTT||||||,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000433134|protein_coding|3/4|c.157+27_157+28delTT||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|IKZF2|ENSG00000030419|transcript|ENST00000452786|protein_coding|3/3|c.139+27_139+28delTT||||||WARNING_TRANSCRIPT_INCOMPLETE;LOF=(IKZF2|ENSG00000030419|17|0.06) GT:AD:AF:DP 0/1:80,4:0.069:84 0/0:31,0:0:31 | |
| chr2 215279313 . C T . t_lod_fstar ClippingRankSum=0;DP=109;ECNT=1;FS=0;HCNT=24;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=6.91;ReadPosRankSum=-1.923;TLOD=4.98;ANN=T|splice_region_variant&intron_variant|LOW|VWC2L|ENSG00000174453|transcript|ENST00000312504|protein_coding|2/3|c.390+6C>T||||||,T|splice_region_variant&intron_variant|LOW|VWC2L|ENSG00000174453|transcript|ENST00000427124|protein_coding|2/2|c.390+6C>T||||||,T|downstream_gene_variant|MODIFIER|SPAG16|ENSG00000144451|transcript|ENST00000331683|protein_coding||c.*4274C>T|||||4088|,T|downstream_gene_variant|MODIFIER|SPAG16|ENSG00000144451|transcript|ENST00000406979|nonsense_mediated_decay||c.*1118545C>T|||||4088|,T|downstream_gene_variant|MODIFIER|SPAG16|ENSG00000144451|transcript|ENST00000374309|protein_coding||c.*4274C>T|||||4274|,T|downstream_gene_variant|MODIFIER|SPAG16|ENSG00000144451|transcript|ENST00000451561|protein_coding||c.*4274C>T|||||4271|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|SPAG16|ENSG00000144451|transcript|ENST00000480494|processed_transcript||n.*4356C>T|||||4356|,T|intron_variant|MODIFIER|AC107218.3|ENSG00000197585|transcript|ENST00000437883|antisense|4/4|n.417+21603G>A||||||,T|intron_variant|MODIFIER|AC107218.3|ENSG00000197585|transcript|ENST00000412896|antisense|3/3|n.303+21603G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|VWC2L|ENSG00000174453|transcript|ENST00000477752|retained_intron|2/2|n.1186C>T|||||| GT:AD:AF:DP 0/1:78,3:0.047:81 0/0:28,0:0:28 | |
| chr2 215875157 . G T . t_lod_fstar ClippingRankSum=0;DP=243;ECNT=1;FS=5.001;HCNT=18;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.30;ReadPosRankSum=2.073;TLOD=4.56;ANN=T|missense_variant|MODERATE|ABCA12|ENSG00000144452|transcript|ENST00000272895|protein_coding|18/53|c.2370C>A|p.Asn790Lys|2590/9100|2370/7788|790/2595||,T|missense_variant|MODERATE|ABCA12|ENSG00000144452|transcript|ENST00000389661|protein_coding|10/45|c.1416C>A|p.Asn472Lys|1575/7005|1416/6834|472/2277|| GT:AD:AF:DP 0/1:174,4:0.023:178 0/0:65,0:0:65 | |
| chr2 216200756 . A T . t_lod_fstar ClippingRankSum=0;DP=333;ECNT=1;FS=0;HCNT=19;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=24.37;ReadPosRankSum=-0.888;TLOD=4.43;ANN=T|splice_acceptor_variant&intron_variant|HIGH|ATIC|ENSG00000138363|transcript|ENST00000236959|protein_coding|10/15|c.1009-2A>T||||||,T|splice_acceptor_variant&intron_variant|HIGH|ATIC|ENSG00000138363|transcript|ENST00000443953|nonsense_mediated_decay|10/15|c.*1106-2A>T||||||,T|splice_acceptor_variant&intron_variant|HIGH|ATIC|ENSG00000138363|transcript|ENST00000540518|protein_coding|10/15|c.832-2A>T||||||,T|splice_acceptor_variant&intron_variant|HIGH|ATIC|ENSG00000138363|transcript|ENST00000435675|protein_coding|9/14|c.1006-2A>T||||||,T|splice_acceptor_variant&intron_variant|HIGH|ATIC|ENSG00000138363|transcript|ENST00000446622|protein_coding|1/5|c.88-2A>T||||||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ATIC|ENSG00000138363|transcript|ENST00000426233|protein_coding|1/5|c.11A>T|p.Gln4Leu|12/713|11/693|4/230||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ATIC|ENSG00000138363|transcript|ENST00000479093|retained_intron||n.-2733A>T|||||2733|,T|upstream_gene_variant|MODIFIER|ATIC|ENSG00000138363|transcript|ENST00000467388|retained_intron||n.-2736A>T|||||2736|,T|upstream_gene_variant|MODIFIER|ATIC|ENSG00000138363|transcript|ENST00000459796|retained_intron||n.-2837A>T|||||2837|,T|downstream_gene_variant|MODIFIER|ATIC|ENSG00000138363|transcript|ENST00000427397|nonsense_mediated_decay||c.*23759A>T|||||1029|;LOF=(ATIC|ENSG00000138363|15|0.33) GT:AD:AF:DP 0/1:208,6:0.021:214 0/0:119,0:0:119 | |
| chr2 216743583 . G T . t_lod_fstar ClippingRankSum=0;DP=116;ECNT=1;FS=23.951;HCNT=86;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.30;ReadPosRankSum=-0.413;TLOD=5.43;ANN=T|non_coding_transcript_exon_variant|MODIFIER|AC122136.1|ENSG00000212055|transcript|ENST00000390766|miRNA|1/1|n.60C>A|||||| GT:AD:AF:DP 0/1:44,6:0.143:50 0/0:64,0:0:64 | |
| chr2 218669258 . A AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT . t_lod_fstar ClippingRankSum=0;DP=59;ECNT=1;FS=0;HCNT=16;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.35;ReadPosRankSum=-0.993;TLOD=5.91;ANN=AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|frameshift_variant|HIGH|TNS1|ENSG00000079308|transcript|ENST00000171887|protein_coding|33/33|c.5131_5132insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|p.Leu1711fs|5584/10331|5131/5208|1711/1735||,AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|frameshift_variant|HIGH|TNS1|ENSG00000079308|transcript|ENST00000446688|protein_coding|15/15|c.2545_2546insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|p.Leu849fs|2545/4292|2545/2622|849/873||WARNING_TRANSCRIPT_NO_START_CODON,AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|frameshift_variant|HIGH|TNS1|ENSG00000079308|transcript|ENST00000419504|protein_coding|31/31|c.5089_5090insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|p.Leu1697fs|5251/5921|5089/5166|1697/1721||,AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|frameshift_variant|HIGH|TNS1|ENSG00000079308|transcript|ENST00000430930|protein_coding|30/30|c.5068_5069insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|p.Leu1690fs|5230/5900|5068/5145|1690/1714||,AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|upstream_gene_variant|MODIFIER|AC009469.1|ENSG00000256309|transcript|ENST00000546295|pseudogene||n.-3280_-3279insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|||||3280|,AGCTCAGCAAAGAGGTGGCAGGCGTTGTCCGTGGTGCTGCCCTGCTTCCGGGCCACGAAGCCT|non_coding_transcript_exon_variant|MODIFIER|TNS1|ENSG00000079308|transcript|ENST00000490566|retained_intron|8/8|n.914_915insAGGCTTCGTGGCCCGGAAGCAGGGCAGCACCACGGACAACGCCTGCCACCTCTTTGCTGAGC|||||| GT:AD:AF:DP 0/1:30,1:0.083:31 0/0:10,0:0:10 | |
| chr2 218824721 . CAGG C . t_lod_fstar ClippingRankSum=0;DP=80;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.40;ReadPosRankSum=1.62;TLOD=5.65;ANN=C|intron_variant|MODIFIER|TNS1|ENSG00000079308|transcript|ENST00000446903|protein_coding|3/18|c.186+18764_186+18766delCCT||||||WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|TNS1|ENSG00000079308|transcript|ENST00000413280|protein_coding|1/7|c.-190+18764_-190+18766delCCT||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:52,4:0.056:56 0/0:14,0:0:14 | |
| chr2 219029400 . G T . t_lod_fstar ClippingRankSum=0;DP=133;ECNT=1;FS=2.416;HCNT=7;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.33;ReadPosRankSum=-0.008;TLOD=5.17;ANN=T|missense_variant|MODERATE|CXCR1|ENSG00000163464|transcript|ENST00000295683|protein_coding|2/2|c.535C>A|p.His179Asn|656/2488|535/1053|179/350|| GT:AD:AF:DP 0/1:81,3:0.05:84 0/0:46,0:0:46 | |
| chr2 219319011 . GACA G . t_lod_fstar ClippingRankSum=0;DP=121;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.70;ReadPosRankSum=0.782;TLOD=5.39;ANN=G|3_prime_UTR_variant|MODIFIER|USP37|ENSG00000135913|transcript|ENST00000258399|protein_coding|26/26|c.*639_*641delTGT|||||639|,G|3_prime_UTR_variant|MODIFIER|USP37|ENSG00000135913|transcript|ENST00000454775|protein_coding|26/26|c.*639_*641delTGT|||||639|,G|3_prime_UTR_variant|MODIFIER|USP37|ENSG00000135913|transcript|ENST00000415516|protein_coding|24/24|c.*639_*641delTGT|||||639|,G|downstream_gene_variant|MODIFIER|VIL1|ENSG00000127831|transcript|ENST00000248444|protein_coding||c.*4953_*4955delACA|||||994|,G|downstream_gene_variant|MODIFIER|VIL1|ENSG00000127831|transcript|ENST00000392114|protein_coding||c.*4953_*4955delACA|||||4765|,G|downstream_gene_variant|MODIFIER|USP37|ENSG00000135913|transcript|ENST00000418019|protein_coding||c.*639_*641delTGT|||||526| GT:AD:AF:DP 0/1:67,3:0.042:70 0/0:30,1:0.042:31 | |
| chr2 220039582 . ACCT A . PASS ClippingRankSum=0;DP=115;ECNT=1;FS=1.983;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=7.82;ReadPosRankSum=0.017;TLOD=8.55;ANN=A|disruptive_inframe_deletion|MODERATE|CNPPD1|ENSG00000115649|transcript|ENST00000360507|protein_coding|5/8|c.425_427delAGG|p.Glu142del|565/2060|425/1233|142/410||,A|disruptive_inframe_deletion|MODERATE|CNPPD1|ENSG00000115649|transcript|ENST00000409789|protein_coding|6/9|c.425_427delAGG|p.Glu142del|855/2073|425/1233|142/410||,A|disruptive_inframe_deletion|MODERATE|CNPPD1|ENSG00000115649|transcript|ENST00000453038|protein_coding|6/9|c.425_427delAGG|p.Glu142del|656/1154|425/925|142/307||WARNING_TRANSCRIPT_INCOMPLETE,A|disruptive_inframe_deletion|MODERATE|CNPPD1|ENSG00000115649|transcript|ENST00000451647|protein_coding|4/7|c.506_508delAGG|p.Glu169del|578/919|506/849|169/282||WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000455516|protein_coding||c.-4879_-4877delAGG|||||4829|,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000430297|protein_coding||c.-3492_-3490delCCT|||||3356|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000498327|retained_intron||n.-4036_-4034delAGG|||||4034|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000318673|nonsense_mediated_decay||c.-4879_-4877delAGG|||||4874|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000396775|protein_coding||c.-5197_-5195delAGG|||||4766|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000295738|protein_coding||c.-4879_-4877delAGG|||||4766|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000409878|protein_coding||c.-4879_-4877delAGG|||||4844|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000497918|retained_intron||n.-4806_-4804delAGG|||||4804|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000409370|protein_coding||c.-4879_-4877delAGG|||||4871|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000465580|retained_intron||n.-4830_-4828delAGG|||||4828|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000430764|protein_coding||c.-4879_-4877delAGG|||||4857|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000421779|nonsense_mediated_decay||c.-4879_-4877delAGG|||||4826|,A|upstream_gene_variant|MODIFIER|SLC23A3|ENSG00000213901|transcript|ENST00000461812|retained_intron||n.-4834_-4832delAGG|||||4832|,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000458520|protein_coding||c.-5875_-5873delCCT|||||1364|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000443757|protein_coding||c.-5875_-5873delCCT|||||3062|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000273048|nonsense_mediated_decay||c.-3492_-3490delCCT|||||3366|,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000452293|nonsense_mediated_decay||c.-3492_-3490delCCT|||||3416|,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000430747|protein_coding||c.-5875_-5873delCCT|||||3853|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000452022|protein_coding||c.-5875_-5873delCCT|||||3866|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|FAM134A|ENSG00000144567|transcript|ENST00000465672|retained_intron||n.-4125_-4123delCCT|||||4125| GT:AD:AF:DP 0/1:67,4:0.059:71 0/0:34,0:0:34 | |
| chr2 223158424 . ACT A . PASS ClippingRankSum=0;DP=305;ECNT=1;FS=2.537;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.01;ReadPosRankSum=1.076;TLOD=10.64;ANN=A|3_prime_UTR_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000409828|protein_coding|4/4|c.*398_*399delAG|||||398|,A|3_prime_UTR_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000258387|protein_coding|5/5|c.*16_*17delAG|||||16|,A|upstream_gene_variant|MODIFIER|CCDC140|ENSG00000163081|transcript|ENST00000295226|protein_coding||c.-10197_-10196delCT|||||4441|,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000392069|protein_coding|4/9|c.586+460_586+461delAG||||||,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000344493|protein_coding|4/7|c.586+460_586+461delAG||||||,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000350526|protein_coding|4/7|c.586+460_586+461delAG||||||,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000336840|protein_coding|4/8|c.586+460_586+461delAG||||||,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000392070|protein_coding|4/8|c.586+460_586+461delAG||||||,A|intron_variant|MODIFIER|PAX3|ENSG00000135903|transcript|ENST00000409551|protein_coding|4/8|c.583+460_583+461delAG|||||| GT:AD:AF:DP 0/1:179,10:0.053:189 0/0:80,2:0.036:82 | |
| chr2 224760359 . TGAGA T . PASS ClippingRankSum=0;DP=48;ECNT=1;FS=0;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.77;ReadPosRankSum=-0.969;TLOD=6.62;ANN=T|upstream_gene_variant|MODIFIER|WDFY1|ENSG00000085449|transcript|ENST00000491453|retained_intron||n.-1186_-1183delTCTC|||||1183|,T|intron_variant|MODIFIER|WDFY1|ENSG00000085449|transcript|ENST00000233055|protein_coding|6/11|c.599-16_599-13delTCTC||||||,T|intron_variant|MODIFIER|WDFY1|ENSG00000085449|transcript|ENST00000493001|retained_intron|1/2|n.320-16_320-13delTCTC||||||,T|intron_variant|MODIFIER|WDFY1|ENSG00000085449|transcript|ENST00000429915|protein_coding|4/5|c.470-16_470-13delTCTC||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:12,3:0.25:15 0/0:16,0:0:16 | |
| chr2 227600452 . CA C . t_lod_fstar ClippingRankSum=0;DP=218;ECNT=1;FS=4.518;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=10.39;ReadPosRankSum=1.005;TLOD=5.81;ANN=C|3_prime_UTR_variant|MODIFIER|IRS1|ENSG00000169047|transcript|ENST00000305123|protein_coding|2/2|c.*535delT|||||59273| GT:AD:AF:DP 0/1:121,8:0.06:129 0/0:68,3:0.041:71 | |
| chr2 227872995 . T C . clustered_events;germline_risk ClippingRankSum=0;DP=15;ECNT=2;FS=6.368;HCNT=2;MAX_ED=33;MIN_ED=33;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.20;ReadPosRankSum=1.518;TLOD=22.43;ANN=C|synonymous_variant|LOW|COL4A4|ENSG00000081052|transcript|ENST00000396625|protein_coding|47/48|c.4548A>G|p.Val1516Val|4756/9895|4548/5073|1516/1690||,C|synonymous_variant|LOW|COL4A4|ENSG00000081052|transcript|ENST00000329662|protein_coding|46/47|c.4539A>G|p.Val1513Val|4747/5272|4539/5064|1513/1687|| GT:AD:AF:DP 0/1:1,10:0.875:11 0/0:4,0:0:4 | |
| chr2 227873028 . A G . clustered_events;germline_risk ClippingRankSum=0;DP=10;ECNT=2;FS=0;HCNT=2;MAX_ED=33;MIN_ED=33;MQ=60;MQ0=0;MQRankSum=0;NLOD=0.602;ReadPosRankSum=-0.253;TLOD=20.46;ANN=G|splice_region_variant&intron_variant|LOW|COL4A4|ENSG00000081052|transcript|ENST00000396625|protein_coding|46/47|c.4523-8T>C||||||,G|splice_region_variant&intron_variant|LOW|COL4A4|ENSG00000081052|transcript|ENST00000329662|protein_coding|45/46|c.4514-8T>C|||||| GT:AD:AF:DP 0/1:0,8:1:8 0/0:2,0:0:2 | |
| chr2 228113279 . ACT A . PASS ClippingRankSum=0;DP=153;ECNT=1;FS=1.78;HCNT=2;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=8.97;ReadPosRankSum=-1.262;TLOD=7.67;ANN=A|intron_variant|MODIFIER|COL4A3|ENSG00000169031|transcript|ENST00000396578|protein_coding|9/51|c.546+56_546+57delCT||||||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000439598|antisense|9/13|n.1593-10391_1593-10390delAG||||||,A|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000606119|antisense|1/1|n.22-10391_22-10390delAG||||||,A|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000437673|antisense|2/2|n.612-10391_612-10390delAG||||||,A|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000396588|antisense|9/9|n.1659-2300_1659-2299delAG|||||| GT:AD:AF:DP 0/1:83,6:0.069:89 0/0:42,0:0:42 | |
| chr2 228172422 . G T . t_lod_fstar ClippingRankSum=0;DP=161;ECNT=1;FS=0;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=9.63;ReadPosRankSum=0.041;TLOD=4.41;ANN=T|splice_region_variant&intron_variant|LOW|COL4A3|ENSG00000169031|transcript|ENST00000396578|protein_coding|47/51|c.4253-4G>T||||||,T|upstream_gene_variant|MODIFIER|COL4A3|ENSG00000169031|transcript|ENST00000469504|processed_transcript||n.-66G>T|||||66|,T|downstream_gene_variant|MODIFIER|COL4A3|ENSG00000169031|transcript|ENST00000468753|processed_transcript||n.*3806G>T|||||3806|,T|downstream_gene_variant|MODIFIER|COL4A3|ENSG00000169031|transcript|ENST00000471862|retained_intron||n.*3378G>T|||||3378|,T|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000439598|antisense|1/13|n.48-2051C>A||||||,T|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000396588|antisense|1/9|n.20-2051C>A||||||,T|intron_variant|MODIFIER|AC097662.2|ENSG00000236432|transcript|ENST00000433324|antisense|1/3|n.34+17462C>A|||||| GT:AD:AF:DP 0/1:106,4:0.038:110 0/0:50,0:0:50 | |
| chr2 228763031 . GTA G . PASS ClippingRankSum=0;DP=332;ECNT=1;FS=0;HCNT=13;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=15.88;ReadPosRankSum=-0.931;TLOD=9.30;ANN=G|downstream_gene_variant|MODIFIER|DAW1|ENSG00000123977|transcript|ENST00000472604|processed_transcript||n.*2725_*2726delTA|||||2725|,G|intron_variant|MODIFIER|DAW1|ENSG00000123977|transcript|ENST00000309931|protein_coding|6/12|c.540+46_540+47delAT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DAW1|ENSG00000123977|transcript|ENST00000373666|protein_coding|6/13|c.540+46_540+47delAT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DAW1|ENSG00000123977|transcript|ENST00000454999|nonsense_mediated_decay|7/7|c.*481+46_*481+47delAT||||||INFO_REALIGN_3_PRIME,G|intron_variant|MODIFIER|DAW1|ENSG00000123977|transcript|ENST00000545118|protein_coding|7/13|c.495+46_495+47delAT||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:169,8:0.047:177 0/0:92,2:0.016:94 | |
| chr2 230655858 . G T . t_lod_fstar ClippingRankSum=0;DP=316;ECNT=1;FS=2.123;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=19.81;ReadPosRankSum=0.494;TLOD=4.27;ANN=T|missense_variant|MODERATE|TRIP12|ENSG00000153827|transcript|ENST00000389044|protein_coding|30/42|c.4444C>A|p.His1482Asn|4613/6405|4444/6123|1482/2040||,T|missense_variant|MODERATE|TRIP12|ENSG00000153827|transcript|ENST00000283943|protein_coding|29/41|c.4300C>A|p.His1434Asn|4479/9874|4300/5979|1434/1992||,T|missense_variant|MODERATE|TRIP12|ENSG00000153827|transcript|ENST00000389045|protein_coding|27/39|c.3490C>A|p.His1164Asn|3563/5355|3490/5169|1164/1722||,T|downstream_gene_variant|MODIFIER|TRIP12|ENSG00000153827|transcript|ENST00000470302|retained_intron||n.*646C>A|||||646|,T|downstream_gene_variant|MODIFIER|TRIP12|ENSG00000153827|transcript|ENST00000495322|retained_intron||n.*832C>A|||||832|,T|downstream_gene_variant|MODIFIER|TRIP12|ENSG00000153827|transcript|ENST00000461189|retained_intron||n.*3719C>A|||||3719| GT:AD:AF:DP 0/1:226,3:0.02:229 0/0:86,0:0:86 | |
| chr2 233243528 . ATGC A . PASS ClippingRankSum=0;DP=173;ECNT=1;FS=0;HCNT=11;MAX_ED=.;MIN_ED=.;MQ=59.84;MQ0=0;MQRankSum=-4.649;NLOD=4.19;ReadPosRankSum=-0.158;TLOD=10.09;ANN=A|conservative_inframe_deletion|MODERATE|ALPP|ENSG00000163283|transcript|ENST00000392027|protein_coding|1/11|c.37_39delCTG|p.Leu13del|306/2971|37/1608|13/535||INFO_REALIGN_3_PRIME,A|upstream_gene_variant|MODIFIER|ALPP|ENSG00000163283|transcript|ENST00000485563|retained_intron||n.-2420_-2418delTGC|||||2420|,A|downstream_gene_variant|MODIFIER|AC068134.8|ENSG00000224516|transcript|ENST00000441266|antisense||n.*814_*816delGCA|||||816|,A|downstream_gene_variant|MODIFIER|AC068134.8|ENSG00000224516|transcript|ENST00000439072|antisense||n.*938_*940delGCA|||||940|,A|non_coding_transcript_exon_variant|MODIFIER|ALPP|ENSG00000163283|transcript|ENST00000474529|retained_intron|1/4|n.116_118delCTG||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:97,5:0.053:102 0/0:55,4:0.048:59 | |
| chr2 233246088 . C T . PASS ClippingRankSum=0;DP=136;ECNT=1;FS=19.748;HCNT=27;MAX_ED=.;MIN_ED=.;MQ=54.46;MQ0=14;MQRankSum=-5.143;NLOD=6.16;ReadPosRankSum=-0.188;TLOD=6.60;ANN=T|upstream_gene_variant|MODIFIER|AC068134.8|ENSG00000224516|transcript|ENST00000439072|antisense||n.-341G>A|||||341|,T|downstream_gene_variant|MODIFIER|ECEL1P2|ENSG00000244280|transcript|ENST00000461596|processed_transcript||n.*4372G>A|||||4372|,T|downstream_gene_variant|MODIFIER|ALPP|ENSG00000163283|transcript|ENST00000474529|retained_intron||n.*1594C>T|||||1594|,T|intron_variant|MODIFIER|ALPP|ENSG00000163283|transcript|ENST00000392027|protein_coding|10/10|c.1309+11C>T||||||,T|intron_variant|MODIFIER|AC068134.8|ENSG00000224516|transcript|ENST00000441266|antisense|1/2|n.200+97G>A||||||,T|intron_variant|MODIFIER|ALPP|ENSG00000163283|transcript|ENST00000485563|retained_intron|1/1|n.129+11C>T|||||| GT:AD:AF:DP 0/1:65,9:0.125:74 0/0:41,5:0.132:46 | |
| chr2 233620984 . CGAG C . t_lod_fstar ClippingRankSum=0;DP=74;ECNT=1;FS=2.989;HCNT=27;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.40;ReadPosRankSum=-0.123;TLOD=5.55;ANN=C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000373566|protein_coding|6/30|c.331_333delGGA|p.Gly111del|528/7878|331/3966|111/1321||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000373563|protein_coding|6/29|c.331_333delGGA|p.Gly111del|526/5847|331/3900|111/1299||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000428883|protein_coding|6/6|c.331_333delGGA|p.Gly111del|529/544|331/346|111/114||WARNING_TRANSCRIPT_INCOMPLETE&INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409480|protein_coding|7/31|c.331_333delGGA|p.Gly111del|593/5976|331/3966|111/1321||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000430720|protein_coding|6/6|c.331_333delGGA|p.Gly111del|554/561|331/338|111/111||WARNING_TRANSCRIPT_INCOMPLETE&INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409547|protein_coding|8/31|c.331_333delGGA|p.Gly111del|642/5978|331/3900|111/1299||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000423659|protein_coding|6/18|c.331_333delGGA|p.Gly111del|500/2329|331/2160|111/719||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409196|protein_coding|5/28|c.331_333delGGA|p.Gly111del|429/5747|331/3882|111/1293||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409451|protein_coding|7/31|c.331_333delGGA|p.Gly111del|557/5937|331/3963|111/1320||INFO_REALIGN_3_PRIME,C|conservative_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000440945|protein_coding|6/21|c.331_333delGGA|p.Gly111del|481/2658|331/2508|111/835||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,C|downstream_gene_variant|MODIFIER|AC064852.4|ENSG00000241409|transcript|ENST00000427571|prime3_overlapping_ncrna||n.*3869_*3871delCTC|||||3871|,C|downstream_gene_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000421433|protein_coding||c.*40_*42delGAG|||||40|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000425040|protein_coding||c.*21_*23delGAG|||||21|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000429187|protein_coding||c.*1_*3delGAG|||||1|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000456491|protein_coding|5/5|c.131-4200_131-4198delGGA||||||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000424038|nonsense_mediated_decay|4/6|c.268-4198_268-4196delGGA||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000463554|processed_transcript|6/9|n.483_485delGGA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:49,2:0.05:51 0/0:23,0:0:23 | |
| chr2 233697763 . TGCA T . germline_risk ClippingRankSum=0;DP=35;ECNT=1;FS=0;HCNT=32;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=1.49;ReadPosRankSum=0.849;TLOD=10.15;ANN=T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000373566|protein_coding|23/30|c.2808_2810delGCA|p.Gln937del|3005/7878|2808/3966|936/1321||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000373563|protein_coding|22/29|c.2742_2744delGCA|p.Gln915del|2937/5847|2742/3900|914/1299||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409480|protein_coding|24/31|c.2808_2810delGCA|p.Gln937del|3070/5976|2808/3966|936/1321||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409547|protein_coding|24/31|c.2742_2744delGCA|p.Gln915del|3053/5978|2742/3900|914/1299||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409196|protein_coding|21/28|c.2724_2726delGCA|p.Gln909del|2822/5747|2724/3882|908/1293||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000409451|protein_coding|24/31|c.2805_2807delGCA|p.Gln936del|3031/5937|2805/3963|935/1320||INFO_REALIGN_3_PRIME,T|disruptive_inframe_deletion|MODERATE|GIGYF2|ENSG00000204120|transcript|ENST00000452341|protein_coding|15/18|c.2235_2237delGCA|p.Gln746del|2316/2913|2235/2619|745/872||INFO_REALIGN_3_PRIME,T|downstream_gene_variant|MODIFIER|Y_RNA|ENSG00000199781|transcript|ENST00000362911|misc_RNA||n.*4303_*4305delGCA|||||4303|,T|non_coding_transcript_exon_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000474312|retained_intron|6/13|n.1777_1779delGCA||||||INFO_REALIGN_3_PRIME,T|non_coding_transcript_exon_variant|MODIFIER|GIGYF2|ENSG00000204120|transcript|ENST00000469843|processed_transcript|1/3|n.199_201delGCA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:16,3:0.188:19 0/0:8,0:0:8 | |
| chr2 234432024 . G T . t_lod_fstar ClippingRankSum=0;DP=202;ECNT=1;FS=4.687;HCNT=8;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.84;ReadPosRankSum=0.07;TLOD=4.46;ANN=T|missense_variant|MODERATE|USP40|ENSG00000085982|transcript|ENST00000450966|protein_coding|15/31|c.2026C>A|p.Pro676Thr|2026/5616|2026/3744|676/1247||,T|missense_variant|MODERATE|USP40|ENSG00000085982|transcript|ENST00000251722|protein_coding|16/32|c.1990C>A|p.Pro664Thr|2108/5692|1990/3708|664/1235||,T|missense_variant|MODERATE|USP40|ENSG00000085982|transcript|ENST00000427112|protein_coding|15/31|c.1990C>A|p.Pro664Thr|2026/3744|1990/3708|664/1235||,T|upstream_gene_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000452724|protein_coding||c.-126C>A|||||126|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000485943|processed_transcript||n.*2133C>A|||||2133| GT:AD:AF:DP 0/1:139,4:0.029:143 0/0:59,0:0:59 | |
| chr2 234471356 . TATA T . PASS ClippingRankSum=0;DP=442;ECNT=1;FS=0;HCNT=14;MAX_ED=.;MIN_ED=.;MQ=59.81;MQ0=0;MQRankSum=-2.136;NLOD=23.15;ReadPosRankSum=-0.896;TLOD=21.40;ANN=T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000450966|protein_coding|2/30|c.303+23_303+25delTAT||||||,T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000251722|protein_coding|3/31|c.267+23_267+25delTAT||||||,T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000427112|protein_coding|2/30|c.267+23_267+25delTAT||||||,T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000427947|retained_intron|3/5|n.313+23_313+25delTAT||||||,T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000484528|retained_intron|3/4|n.385+23_385+25delTAT||||||,T|intron_variant|MODIFIER|USP40|ENSG00000085982|transcript|ENST00000443711|protein_coding|3/3|c.267+23_267+25delTAT|||||| GT:AD:AF:DP 0/1:274,10:0.041:284 0/0:133,1:0.011:134 | |
| chr2 234668879 . CAT C . t_lod_fstar ClippingRankSum=0;DP=38;ECNT=1;FS=5.975;HCNT=6;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=2.40;ReadPosRankSum=0.469;TLOD=4.08;ANN=C|upstream_gene_variant|MODIFIER|AC114812.5|ENSG00000178836|transcript|ENST00000450901|processed_transcript||n.-4901_-4900delAT|||||4900|,C|upstream_gene_variant|MODIFIER|UGT1A1|ENSG00000242366|transcript|ENST00000305208|protein_coding||c.-54_-53delAT|||||14|,C|upstream_gene_variant|MODIFIER|AC114812.5|ENSG00000178836|transcript|ENST00000421868|processed_transcript||n.-4890_-4889delAT|||||4889|,C|upstream_gene_variant|MODIFIER|AC114812.5|ENSG00000178836|transcript|ENST00000389816|processed_transcript||n.-4966_-4965delAT|||||4965|,C|upstream_gene_variant|MODIFIER|AC114812.5|ENSG00000178836|transcript|ENST00000449669|transcribed_processed_pseudogene||n.-4966_-4965delAT|||||4965|,C|upstream_gene_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000360418|protein_coding||c.-54_-53delAT|||||54|,C|upstream_gene_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000608383|protein_coding||c.-54_-53delAT|||||54|,C|downstream_gene_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000480628|processed_transcript||n.*3883_*3884delAT|||||3883|,C|intron_variant|MODIFIER|UGT1A10|ENSG00000242515|transcript|ENST00000344644|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A9|ENSG00000241119|transcript|ENST00000354728|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A7|ENSG00000244122|transcript|ENST00000373426|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000305139|protein_coding|1/4|c.862-6787_862-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A5|ENSG00000240224|transcript|ENST00000373414|protein_coding|1/4|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000608381|protein_coding|1/4|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A4|ENSG00000244474|transcript|ENST00000373409|protein_coding|1/4|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A3|ENSG00000243135|transcript|ENST00000482026|protein_coding|1/4|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000373450|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A10|ENSG00000242515|transcript|ENST00000373445|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000609637|protein_coding|1/4|c.856-6787_856-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000373424|protein_coding|2/5|c.61-6787_61-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000446481|nonsense_mediated_decay|2/6|c.61-6787_61-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000484784|nonsense_mediated_decay|2/2|c.*238-6787_*238-6786delTA||||||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A6|ENSG00000167165|transcript|ENST00000406651|protein_coding|1/4|c.61-6787_61-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A4|ENSG00000244474|transcript|ENST00000450233|nonsense_mediated_decay|1/5|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|UGT1A8|ENSG00000241635|transcript|ENST00000609767|protein_coding|1/4|c.868-6787_868-6786delTA||||||INFO_REALIGN_3_PRIME GT:AD:AF:DP 0/1:23,3:0.111:26 0/0:10,0:0:10 | |
| chr2 238271882 . T TAA . t_lod_fstar ClippingRankSum=0;DP=153;ECNT=1;FS=0;HCNT=22;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.10;ReadPosRankSum=1.709;TLOD=4.88;ANN=TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000295550|protein_coding|14/43|c.6063+12_6063+13dupTT||||||,TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000347401|protein_coding|13/42|c.5460+12_5460+13dupTT||||||,TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000353578|protein_coding|13/42|c.5445+12_5445+13dupTT||||||,TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000472056|protein_coding|11/40|c.4242+12_4242+13dupTT||||||,TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000409809|protein_coding|12/41|c.5445+12_5445+13dupTT||||||,TAA|intron_variant|MODIFIER|COL6A3|ENSG00000163359|transcript|ENST00000346358|protein_coding|13/42|c.5463+12_5463+13dupTT|||||| GT:AD:AF:DP 0/1:36,6:0.135:42 0/0:18,1:0.059:19 | |
| chr2 240011729 . G T . t_lod_fstar ClippingRankSum=0;DP=169;ECNT=1;FS=2.327;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=11.14;ReadPosRankSum=0.524;TLOD=5.10;ANN=T|missense_variant|MODERATE|HDAC4|ENSG00000068024|transcript|ENST00000345617|protein_coding|18/27|c.2349C>A|p.Phe783Leu|3141/8976|2349/3255|783/1084||,T|missense_variant|MODERATE|HDAC4|ENSG00000068024|transcript|ENST00000543185|protein_coding|12/21|c.1101C>A|p.Phe367Leu|1711/2707|1101/2007|367/668||,T|upstream_gene_variant|MODIFIER|AC017028.8|ENSG00000265891|transcript|ENST00000582701|miRNA||n.-4237C>A|||||4237|,T|upstream_gene_variant|MODIFIER|MIR4441|ENSG00000264810|transcript|ENST00000582623|miRNA||n.-4107C>A|||||4107|,T|upstream_gene_variant|MODIFIER|AC017028.7|ENSG00000265416|transcript|ENST00000579869|miRNA||n.-3591C>A|||||3591|,T|downstream_gene_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000495497|retained_intron||n.*1111C>A|||||1111|,T|downstream_gene_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000541256|protein_coding||c.*4950C>A|||||4466|,T|downstream_gene_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000493582|retained_intron||n.*4541C>A|||||4541|,T|downstream_gene_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000535493|retained_intron||n.*4857C>A|||||4857|,T|non_coding_transcript_exon_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000487617|retained_intron|4/8|n.256C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|HDAC4|ENSG00000068024|transcript|ENST00000463007|retained_intron|17/17|n.2801C>A|||||| GT:AD:AF:DP 0/1:111,3:0.038:114 0/0:55,0:0:55 | |
| chr2 240969640 . C T . t_lod_fstar ClippingRankSum=0;DP=119;ECNT=1;FS=9.336;HCNT=12;MAX_ED=.;MIN_ED=.;MQ=50.71;MQ0=15;MQRankSum=-2.134;NLOD=2.74;ReadPosRankSum=1.379;TLOD=4.16;ANN=T|synonymous_variant|LOW|OR6B2|ENSG00000182083|transcript|ENST00000402971|protein_coding|1/1|c.207G>A|p.Leu69Leu|267/1066|207/939|69/312||,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000307300|protein_coding||c.-4922G>A|||||4899|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000252711|protein_coding||c.-4922G>A|||||4821|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000404554|protein_coding||c.-4922G>A|||||4917|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000485344|retained_intron||n.-4900G>A|||||4900|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000443626|protein_coding||c.-4922G>A|||||4880|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000414580|nonsense_mediated_decay||c.-4922G>A|||||4910|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000407129|protein_coding||c.-4922G>A|||||4916|,T|upstream_gene_variant|MODIFIER|NDUFA10|ENSG00000130414|transcript|ENST00000497536|retained_intron||n.-4899G>A|||||4899| GT:AD:AF:DP 0/1:66,4:0.067:70 0/0:27,3:0.091:30 | |
| chr2 241700142 . G A . t_lod_fstar ClippingRankSum=0;DP=32;ECNT=1;FS=0;HCNT=4;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=3.61;ReadPosRankSum=0.39;TLOD=4.39;ANN=A|missense_variant|MODERATE|KIF1A|ENSG00000130294|transcript|ENST00000498729|protein_coding|25/50|c.2384C>T|p.Ala795Val|2631/9162|2384/5376|795/1791||,A|missense_variant|MODERATE|KIF1A|ENSG00000130294|transcript|ENST00000320389|protein_coding|24/47|c.2357C>T|p.Ala786Val|2516/8832|2357/5073|786/1690||,A|missense_variant|MODERATE|KIF1A|ENSG00000130294|transcript|ENST00000404283|protein_coding|24/42|c.2384C>T|p.Ala795Val|2384/4414|2384/4414|795/1470||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:13,2:0.182:15 0/0:17,0:0:17 | |
| chr2 242035580 . ACTC A . PASS ClippingRankSum=0;DP=202;ECNT=1;FS=3.735;HCNT=3;MAX_ED=.;MIN_ED=.;MQ=60;MQ0=0;MQRankSum=0;NLOD=13.22;ReadPosRankSum=0.028;TLOD=7.84;ANN=A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:A_141-B_326:ENST00000474844-ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:C_141-E_326:ENST00000474844-ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:D_141-G_326:ENST00000474844-ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:F_141-H_326:ENST00000474844-ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FZV:A_141-B_326:ENST00000474844-ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:A_141-B_326:ENST00000474844-ENST00000391980|protein_coding|4/4|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:C_141-E_326:ENST00000474844-ENST00000391980|protein_coding|4/4|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:D_141-G_326:ENST00000474844-ENST00000391980|protein_coding|4/4|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FP9:F_141-H_326:ENST00000474844-ENST00000391980|protein_coding|4/4|c.976_978delGAG||||||,A|protein_protein_contact|HIGH|MTERFD2|ENSG00000122085|interaction|4FZV:A_141-B_326:ENST00000474844-ENST00000391980|protein_coding|4/4|c.976_978delGAG||||||,A|conservative_inframe_deletion|MODERATE|MTERFD2|ENSG00000122085|transcript|ENST00000241527|nonsense_mediated_decay|4/7|c.976_978delGAG|p.Glu326del|1000/4529|976/1146|326/381||,A|conservative_inframe_deletion|MODERATE|MTERFD2|ENSG00000122085|transcript|ENST00000391980|protein_coding|4/4|c.976_978delGAG|p.Glu326del|1037/1637|976/1146|326/381||,A|conservative_inframe_deletion|MODERATE|MTERFD2|ENSG00000122085|transcript|ENST00000406593|protein_coding|3/3|c.412_414delGAG|p.Glu138del|505/802|412/582|138/193||,A|conservative_inframe_deletion|MODERATE|MTERFD2|ENSG00000122085|transcript|ENST00000439144|protein_coding|4/4|c.535_537delGAG|p.Glu179del|557/583|535/563|179/186||WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000496878|retained_intron||n.-495_-493delGAG|||||493|,A|upstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000488567|processed_transcript||n.-98_-96delGAG|||||96|,A|upstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000449133|protein_coding||c.-1792_-1790delGAG|||||1790|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000479205|processed_transcript||n.-1736_-1734delGAG|||||1734|,A|downstream_gene_variant|MODIFIER|SNED1|ENSG00000162804|transcript|ENST00000310397|protein_coding||c.*7765_*7767delCTC|||||598|,A|downstream_gene_variant|MODIFIER|SNED1|ENSG00000162804|transcript|ENST00000342631|protein_coding||c.*7765_*7767delCTC|||||3098|,A|downstream_gene_variant|MODIFIER|SNED1|ENSG00000162804|transcript|ENST00000405547|protein_coding||c.*7765_*7767delCTC|||||603|,A|downstream_gene_variant|MODIFIER|SNED1|ENSG00000162804|transcript|ENST00000466618|retained_intron||n.*4313_*4315delCTC|||||4313|,A|downstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000424798|protein_coding||c.*456_*458delGAG|||||435|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000460915|retained_intron||n.*758_*760delGAG|||||760|,A|downstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000407095|protein_coding||c.*1021_*1023delGAG|||||1021|,A|downstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000475860|retained_intron||n.*3000_*3002delGAG|||||3002|,A|downstream_gene_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000434791|protein_coding||c.*3231_*3233delGAG|||||3233|WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000464344|processed_transcript|1/4|n.81-1736_81-1734delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000455202|processed_transcript|2/4|n.264+1075_264+1077delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000480298|processed_transcript|1/2|n.59+6085_59+6087delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000476564|retained_intron|1/3|n.69-1736_69-1734delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000495694|protein_coding|2/4|c.520+3228_520+3230delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000493169|processed_transcript|2/4|n.265+1075_265+1077delGAG||||||,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000414146|protein_coding|3/4|c.262+225_262+227delGAG||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|MTERFD2|ENSG00000122085|transcript|ENST00000401626|protein_coding|2/2|c.521-1736_521-1734delGAG||||||WARNING_TRANSCRIPT_INCOMPLETE GT:AD:AF:DP 0/1:118,6:0.034:124 0/0:59,0:0:59 | |
| chr2 243061070 . C A . PASS ClippingRankSum=0;DP=374;ECNT=1;FS=9.058;HCNT=19;MAX_ED=.;MIN_ED=.;MQ=58.03;MQ0=2;MQRankSum=-5.158;NLOD=7.19;ReadPosRankSum=1.411;TLOD=9.27;ANN=A|upstream_gene_variant|MODIFIER|AC134873.1|ENSG00000244528|transcript|ENST00000453405|processed_pseudogene||n.-3368C>A|||||3368|,A|upstream_gene_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000433444|processed_transcript||n.-3374C>A|||||3374|,A|downstream_gene_variant|MODIFIER|CICP10|ENSG00000224160|transcript|ENST00000439497|processed_pseudogene||n.*937G>T|||||937|,A|downstream_gene_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000444990|retained_intron||n.*2547C>A|||||2547|,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000456398|processed_transcript|4/7|n.464-46C>A||||||,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000403324|processed_transcript|2/4|n.260-46C>A||||||,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000431796|processed_transcript|3/4|n.354-46C>A||||||,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000453598|transcribed_unprocessed_pseudogene|3/7|n.354-46C>A||||||,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000442213|processed_transcript|3/5|n.350+4178C>A||||||,A|intron_variant|MODIFIER|AC093642.5|ENSG00000220804|transcript|ENST00000416103|transcribed_unprocessed_pseudogene|3/3|n.288-46C>A|||||| GT:AD:AF:DP 0/1:249,10:0.033:259 0/0:104,7:0.063:111 | |
| chr3 5164189 . T G . clustered_events;t_lod_fstar ClippingRankSum=0;DP=90;ECNT=2;FS=0;HCNT=2;MAX_ED=12;MIN_ED=12;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.42;ReadPosRankSum=0.239;TLOD=4.31;ANN=G|missense_variant|MODERATE|ARL8B|ENSG00000134108|transcript|ENST00000429403|nonsense_mediated_decay|1/5|c.211T>G|p.Phe71Val|256/709|211/309|71/102||,G|missense_variant|MODERATE|ARL8B|ENSG00000134108|transcript|ENST00000455168|nonsense_mediated_decay|1/7|c.211T>G|p.Phe71Val|213/1641|211/312|71/103||,G|synonymous_variant|LOW|ARL8B|ENSG00000134108|transcript|ENST00000256496|protein_coding|1/7|c.39T>G|p.Arg13Arg|285/3005|39/561|13/186||,G|synonymous_variant|LOW|ARL8B|ENSG00000134108|transcript|ENST00000419534|protein_coding|1/5|c.39T>G|p.Arg13Arg|209/1684|39/492|13/163||,G|non_coding_transcript_exon_variant|MODIFIER|ARL8B|ENSG00000134108|transcript|ENST00000444332|retained_intron|1/2|n.213T>G|||||| GT:AD:AF:DP:PGT:PID 0/1:62,3:0.049:65:0|1:5164189_T_G 0/0:24,0:0:24:0|1:5164189_T_G | |
| chr3 5164201 . G A . clustered_events;t_lod_fstar ClippingRankSum=0;DP=86;ECNT=2;FS=0;HCNT=2;MAX_ED=12;MIN_ED=12;MQ=60;MQ0=0;MQRankSum=0;NLOD=5.12;ReadPosRankSum=0.501;TLOD=4.25;ANN=A|stop_gained|HIGH|ARL8B|ENSG00000134108|transcript|ENST00000256496|protein_coding|1/7|c.51G>A|p.Trp17*|297/3005|51/561|17/186||,A|stop_gained|HIGH|ARL8B|ENSG00000134108|transcript|ENST00000419534|protein_coding|1/5|c.51G>A|p.Trp17*|221/1684|51/492|17/163||,A|missense_variant|MODERATE|ARL8B|ENSG00000134108|transcript|ENST00000429403|nonsense_mediated_decay|1/5|c.223G>A|p.Glu75Lys|268/709|223/309|75/102||,A|missense_variant|MODERATE|ARL8B|ENSG00000134108|transcript|ENST00000455168|nonsense_mediated_decay|1/7|c.223G>A|p.Glu75Lys|225/1641|223/312|75/103||,A|non_coding_transcript_exon_variant|MODIFIER|ARL8B|ENSG00000134108|transcript|ENST00000444332|retained_intron|1/2|n.225G>A||||||;LOF=(ARL8B|ENSG00000134108|7|0.29);NMD=(ARL8B|ENSG00000134108|7|0.29) GT:AD:AF:DP:PGT:PID 0/1:64,2:0.04 |
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