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variant annotation proposal
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| { | |
| "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" | |
| } | |
| ] | |
| } | |
| } | |
| } | |
| ] | |
| } |
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