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reece/GA4GH_prototype_annotations2

Last active August 29, 2015 14:20
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GA4GH_prototype_annotations2.docx, sent by Sarah Hunt to ga4gh-dwg-annotation@googlegroups.com on May 7
Raw
GA4GH_prototype_annotations2
'variantannotations' => [
{
'created' => '1430919899622',
'id' => 'subs',
'transcriptEffects' => [
{
'featureId' => 'ENST00000390914',
'IMPACT' => 'MODIFIER',
'alternateSequence' => 'C',
'effects' => [
'downstream_gene_variant'
],
'HGVSg' => '22:g.16275238T>C',
'id' => 'placeholder_annot_id',
'annotationSetId' => 'Ensembl_79_GRCh37'
},
{
'cDNALocation' => {
'overlapStart' => 1292,
'overlapEnd' => 1293
},
'IMPACT' => 'MODIFIER',
'alternateSequence' => 'C',
'HGVSc' => 'ENST00000452800.1:c.*382C>G',
'effects' => [
'3_prime_UTR_variant,NMD_transcript_variant'
],
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000452800',
'HGVSg' => '22:g.16275238T>C',
'id' => 'placeholder_annot_id'
},
{
'IMPACT' => 'MODIFIER',
'alternateSequence' => 'C',
'HGVSc' => 'ENST00000422014.1:n.444+235T>C',
'effects' => [
'intron_variant,non_coding_transcript_variant'
],
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000422014',
'HGVSg' => '22:g.16275238T>C',
'id' => 'placeholder_annot_id'
},
{
'cDNALocation' => {
'overlapStart' => 1256,
'overlapEnd' => 1257
},
'cdsLocation' => {
'overlapStart' => 1204,
'alternateSequence' => 'atG',
'referenceSequence' => 'atA',
'overlapEnd' => 1205
},
'IMPACT' => 'MODERATE',
'proteinLocation' => {
'overlapStart' => 400,
'alternateSequence' => 'M',
'referenceSequence' => 'I',
'overlapEnd' => 401
},
'alternateSequence' => 'C',
'HGVSc' => 'ENST00000343518.6:c.1206A>G',
'effects' => [
'missense_variant'
],
'HGVSp' => 'ENSP00000340610.6:p.Ile402Met',
'analysisResults' => [
{
'analysisScore' => '1',
'analysisResult' => 'tolerated',
'analysis' => {
'info' => {
'protein database' => 'UniRef90 2014_11'
},
'software' => 'SIFT.5.2.2',
'id' => 'placeholder',
'description' => 'SIFT'
}
},
{
'analysisScore' => '0.004',
'analysisResult' => 'benign',
'analysis' => {
'info' => {
'protein database' => 'UniRef100 Release 2011_12'
},
'software' => 'Polyphen.2.2.2_r405',
'id' => 'placeholder',
'description' => 'Polyphen'
}
}
],
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000343518',
'HGVSg' => '22:g.16275238T>C',
'id' => 'placeholder_annot_id'
}
],
'coLocatedVariants' => [
'rs2845214'
]
},
{
'created' => '1430919901656',
'id' => 'del',
'transcriptEffects' => [
{
'IMPACT' => 'MODIFIER',
'alternateSequence' => '-',
'HGVSc' => 'ENST00000520505.1:n.87-67delT',
'effects' => [
'intron_variant,non_coding_transcript_variant'
],
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000520505',
'HGVSg' => '22:g.17447140delG',
'id' => 'placeholder_annot_id'
},
{
'cDNALocation' => {
'overlapStart' => 1836,
'overlapEnd' => 1837
},
'IMPACT' => 'MODIFIER',
'alternateSequence' => '-',
'HGVSc' => 'ENST00000465611.1:c.*1264delC',
'effects' => [
'3_prime_UTR_variant,NMD_transcript_variant'
],
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000465611',
'HGVSg' => '22:g.17447140delG',
'id' => 'placeholder_annot_id'
},
{
'cDNALocation' => {
'overlapStart' => 1244,
'overlapEnd' => 1245
},
'cdsLocation' => {
'overlapStart' => 1136,
'alternateSequence' => 'ag',
'referenceSequence' => 'Cag',
'overlapEnd' => 1137
},
'IMPACT' => 'HIGH',
'proteinLocation' => {
'overlapStart' => 378,
'alternateSequence' => 'X',
'referenceSequence' => 'Q',
'overlapEnd' => 379
},
'alternateSequence' => '-',
'HGVSc' => 'ENST00000400588.1:c.1138delA',
'effects' => [
'frameshift_variant'
],
'HGVSp' => 'ENSP00000383431.1:p.Gln380ArgfsTer58',
'annotationSetId' => 'Ensembl_79_GRCh37',
'featureId' => 'ENST00000400588',
'HGVSg' => '22:g.17447140delG',
'id' => 'placeholder_annot_id'
},
{
'featureId' => 'ENST00000523144',
'IMPACT' => 'MODIFIER',
'alternateSequence' => '-',
'effects' => [
'downstream_gene_variant'
],
'HGVSg' => '22:g.17447140delG',
'id' => 'placeholder_annot_id',
'annotationSetId' => 'Ensembl_79_GRCh37'
}
]
}
]
}
Raw
json reformmating of above
{
"variantannotations" : [
{
"created" : "1430919899622",
"id" : "subs",
"transcriptEffects" : [
{
"featureId" : "ENST00000390914",
"IMPACT" : "MODIFIER",
"alternateSequence" : "C",
"effects" : [
"downstream_gene_variant"
],
"HGVSg" : "22:g.16275238T>C",
"id" : "placeholder_annot_id",
"annotationSetId" : "Ensembl_79_GRCh37"
},
{
"cDNALocation" : {
"overlapStart" : "1292",
"overlapEnd" : "1293"
},
"IMPACT" : "MODIFIER",
"alternateSequence" : "C",
"HGVSc" : "ENST00000452800.1:c.*382C>G",
"effects" : [
"3_prime_UTR_variant,NMD_transcript_variant"
],
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000452800",
"HGVSg" : "22:g.16275238T>C",
"id" : "placeholder_annot_id"
},
{
"IMPACT" : "MODIFIER",
"alternateSequence" : "C",
"HGVSc" : "ENST00000422014.1:n.444+235T>C",
"effects" : [
"intron_variant,non_coding_transcript_variant"
],
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000422014",
"HGVSg" : "22:g.16275238T>C",
"id" : "placeholder_annot_id"
},
{
"cDNALocation" : {
"overlapStart" : "1256",
"overlapEnd" : "1257"
},
"cdsLocation" : {
"overlapStart" : "1204",
"alternateSequence" : "atG",
"referenceSequence" : "atA",
"overlapEnd" : "1205"
},
"IMPACT" : "MODERATE",
"proteinLocation" : {
"overlapStart" : "400",
"alternateSequence" : "M",
"referenceSequence" : "I",
"overlapEnd" : "401"
},
"alternateSequence" : "C",
"HGVSc" : "ENST00000343518.6:c.1206A>G",
"effects" : [
"missense_variant"
],
"HGVSp" : "ENSP00000340610.6:p.Ile402Met",
"analysisResults" : [
{
"analysisScore" : "1",
"analysisResult" : "tolerated",
"analysis" : {
"info" : {
"protein database" : "UniRef90 2014_11"
},
"software" : "SIFT.5.2.2",
"id" : "placeholder",
"description" : "SIFT"
}
},
{
"analysisScore" : "0.004",
"analysisResult" : "benign",
"analysis" : {
"info" : {
"protein database" : "UniRef100 Release 2011_12"
},
"software" : "Polyphen.2.2.2_r405",
"id" : "placeholder",
"description" : "Polyphen"
}
}
],
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000343518",
"HGVSg" : "22:g.16275238T>C",
"id" : "placeholder_annot_id"
}
],
"coLocatedVariants" : [
"rs2845214"
]
},
{
"created" : "1430919901656",
"id" : "del",
"transcriptEffects" : [
{
"IMPACT" : "MODIFIER",
"alternateSequence" : "-",
"HGVSc" : "ENST00000520505.1:n.87-67delT",
"effects" : [
"intron_variant,non_coding_transcript_variant"
],
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000520505",
"HGVSg" : "22:g.17447140delG",
"id" : "placeholder_annot_id"
},
{
"cDNALocation" : {
"overlapStart" : "1836",
"overlapEnd" : "1837"
},
"IMPACT" : "MODIFIER",
"alternateSequence" : "-",
"HGVSc" : "ENST00000465611.1:c.*1264delC",
"effects" : [
"3_prime_UTR_variant,NMD_transcript_variant"
],
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000465611",
"HGVSg" : "22:g.17447140delG",
"id" : "placeholder_annot_id"
},
{
"cDNALocation" : {
"overlapStart" : "1244",
"overlapEnd" : "1245"
},
"cdsLocation" : {
"overlapStart" : "1136",
"alternateSequence" : "ag",
"referenceSequence" : "Cag",
"overlapEnd" : "1137"
},
"IMPACT" : "HIGH",
"proteinLocation" : {
"overlapStart" : "378",
"alternateSequence" : "X",
"referenceSequence" : "Q",
"overlapEnd" : "379"
},
"alternateSequence" : "-",
"HGVSc" : "ENST00000400588.1:c.1138delA",
"effects" : [
"frameshift_variant"
],
"HGVSp" : "ENSP00000383431.1:p.Gln380ArgfsTer58",
"annotationSetId" : "Ensembl_79_GRCh37",
"featureId" : "ENST00000400588",
"HGVSg" : "22:g.17447140delG",
"id" : "placeholder_annot_id"
},
{
"featureId" : "ENST00000523144",
"IMPACT" : "MODIFIER",
"alternateSequence" : "-",
"effects" : [
"downstream_gene_variant"
],
"HGVSg" : "22:g.17447140delG",
"id" : "placeholder_annot_id",
"annotationSetId" : "Ensembl_79_GRCh37"
}
]
}
]
}
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