cat-vrs/examples/json/functionVariant-ex1.json at v1 · ga4gh/cat-vrs · GitHub

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{
  "id": "civic.mpid:4428",
  "type": "CategoricalVariant",
  "name": "NRAS functionally normal variants",
  "description": "An example categorical variant that uses FeatureContextConstraint and FunctionConstraint.",
  "constraints": [
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "id": "hgnc:7989",
        "conceptType": "Gene",
        "name": "NRAS",
        "primaryCoding": {
          "id": "hgnc:7989",
          "name": "NRAS",
          "system": "https://www.genenames.org",
          "code": "HGNC:7989",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:7989"
          ]
        }
      }
    },
    {
      "type": "FunctionConstraint",
      "functionConsequence": {
        "id": "SO:0002219",
        "name": "functionally normal",
        "primaryCoding": {
          "id": "SO:0002219",
          "name": "functionally_normal",
          "system": "http://www.sequenceontology.org",
          "code": "SO:0002219",
          "iris": [
            "http://www.sequenceontology.org/browser/current_release/term/SO:0002219"
          ]
        }
      },
      "description": "Function consequence described as functionally normal using Sequence Ontology."
    }
  ],
  "members": [
    {
      "id": "ga4gh:VA.GSV_U1hzMrHMWEMEqj-22KMJ9KBjzg3G",
      "type": "Allele",
      "name": "NM_002524.5:c.170A>C",
      "description": "VRS variation of NM_002524.5(NRAS):c.170A>C(p.D57A), generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
      "digest": "GSV_U1hzMrHMWEMEqj-22KMJ9KBjzg3G",
      "expressions": [
        {
          "syntax": "hgvs.c",
          "value": "NM_002524.5:c.170A>C"
        }
      ],
      "location": {
        "id": "ga4gh:SL.giseM38uWBFp7prflNpHkr6HP_8xsCdj",
        "description": "Coding DNA (cDNA) position 170 of the NRAS MANE Select coding transcript (refseq:NM_002524.5), corresponding to genomic position 114713920 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38, 1-based, genomic position",
            "value": "chr1:114713920",
            "description": "Genomic position 114,713,920 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
          },
          {
            "name": "GRCh38, 1-based, inclusive interval notation",
            "value": "chr1:114713920-114713920",
            "description": "Genomic position 114,713,920 to 114,713,920 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
          },
          {
            "name": "GRCh38, 0-based, half-open interval notation",
            "value": "chr1:114713919-114713920",
            "description": "Genomic position 114,713,919 to 114,713,920 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
          }
        ],
        "type": "SequenceLocation",
        "digest": "giseM38uWBFp7prflNpHkr6HP_8xsCdj",
        "sequenceReference": {
          "id": "refseq:NM_002524.5",
          "name": "NM_002524.5",
          "description": "The MANE Select (GRCh38) coding transcript for NRAS.",
          "aliases": [
            "ensembl:ENST00000369535.5",
            "ga4gh:SQ.sMBMPz32WlhQGTxBagnyMCUdy2OD2M--"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.sMBMPz32WlhQGTxBagnyMCUdy2OD2M--",
          "residueAlphabet": "na"
        },
        "start": 300,
        "end": 301,
        "sequence": "A"
      },
      "state": {
        "type": "LiteralSequenceExpression",
        "sequence": "C"
      }
    }
  ]
}