variant annotation proposal

Alternative variant annotation proposal

{
  "loci": [
    {
      "ac": "NC_000003.11",
      "ref": "T",
      "alt": "C",
      "HGVSg": "NC_000004.14:g.57232242T>C",
      "annotations": {
        "aliases": {
          "dbSNP": [
            {
              "name": "rs12345",
              "url": "http://..."
            },
            {
              "name": "rs98765",
              "url": "http://..."
            }
          ],
          "COSMIC": [
            {
              "name": "COST17510",
              "url": "http://cancer.sanger.ac.uk/cosmic/rearrangement/overview?id=17510"
            }
          ]
        },
        "vep": {
          "version": "79",
          "ran_on": "1430919899622",
          "predictions": [
            {
              "canonical": "True",
              "ccds": "CCDS2881.1",
              "cdna-pos": "578",
              "cds-pos": "541",
              "codon-change": "Aca/Gca",
              "consequence": "missense_variant",
              "feature": "ENST00000295934",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1",
              "hgvsc": "ENST00000295934:c.541A>G",
              "hgvsp": "ENSP00000295934:p.Thr181Ala",
              "polyphen-prediction": "benign",
              "polyphen-score": "0",
              "pro-pos": "181",
              "refseq": "NM_003865.2",
              "refseq-hgvsc": "NM_003865.2:c.541A>G",
              "refseq-hgvsp": "NP_003856.1:p.Thr181Ala",
              "sift-prediction": "tolerated",
              "sift-score": "0.11"
            },
            {
              "aa-change": "T/A",
              "canonical": "False",
              "cdna-pos": "459",
              "cds-pos": "439",
              "codon-change": "Aca/Gca",
              "consequence": "missense_variant",
              "feature": "ENST00000473921",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1",
              "hgvsc": "ENST00000473921:c.439A>G",
              "hgvsp": "ENSP00000418918:p.Thr147Ala",
              "polyphen-prediction": "benign",
              "polyphen-score": "0.004",
              "pro-pos": "147",
              "sift-prediction": "tolerated",
              "sift-score": "0.15"
            },
            {
              "canonical": "False",
              "consequence": "downstream_gene_variant",
              "feature": "ENST00000495160",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1"
            }
          ]
        },
        "snpeff": {
          "version": "4.1E",
          "predictions": []
        },
        "ESP": {
          "version": "ESP6500SI-V2",
          "frequencies": [
            {
              "CEU": "0.48"
            },
            {
              "YRI": "0.12"
            }
          ]
        },
        "ClinVar": {
          "version": "",
          "ran_on": "2015-05-01",
          "annotions": []
        },
        "LinkGenerator": {
          "version": "1922-11-22",
          "links": [
            {
              "uri": "http://blah.com/NC_000004.14:g.57232242T>C",
              "title": "Click Here"
            }
          ]
        }
      }
    },
    {
      "ac": "NC_000003.11",
      "ref": "T",
      "alt": "G",
      "HGVSg": "NC_000004.14:g.57232253T>G",
      "annotations": {
        "vep": {
          "version": "79",
          "ran_on": "1430919899622",
          "predictions": [
            {
              "aa-change": "K/T",
              "canonical": "True",
              "ccds": "CCDS2881.1",
              "cdna-pos": "567",
              "cds-pos": "530",
              "codon-change": "aAa/aCa",
              "consequence": "missense_variant",
              "feature": "ENST00000295934",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1",
              "hgvsc": "ENST00000295934:c.530A>C",
              "hgvsp": "ENSP00000295934:p.Lys177Thr",
              "polyphen-prediction": "benign",
              "polyphen-score": "0.139",
              "pro-pos": "177",
              "refseq-hgvsc": "NM_003865.2:c.530A>C",
              "refseq-hgvsp": "NP_003856.1:p.Lys177Thr",
              "sift-prediction": "tolerated",
              "sift-score": "0.34"
            },
            {
              "aa-change": "K/T",
              "canonical": "False",
              "cdna-pos": "448",
              "cds-pos": "428",
              "codon-change": "aAa/aCa",
              "consequence": "missense_variant",
              "feature": "ENST00000473921",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1",
              "hgvsc": "ENST00000473921:c.428A>C",
              "hgvsp": "ENSP00000418918:p.Lys143Thr",
              "polyphen-prediction": "possibly_damaging",
              "polyphen-score": "0.479",
              "pro-pos": "143",
              "sift-prediction": "tolerated",
              "sift-score": "0.06"
            },
            {
              "canonical": "False",
              "consequence": "downstream_gene_variant",
              "feature": "ENST00000495160",
              "feature-type": "Transcript",
              "gene": "ENSG00000163666",
              "hgnc": "HESX1"
            }
          ]
        }
      }
    }
  ]
}