v::NTRK1(hgnc:8031)

Source: CIViC feature id 62026: v::NTRK1 Fusion

Recipes that this example satisfies: None

Attributes

• id: civic.fid:62026, where fid stands for Feature ID, derived from the Feature ID contained within the CIViC URL for this genomic alteration.

• type: CategoricalVariant, as required by the specification.

• name: v::NTRK1(hgnc:8031), the human-readable label given to the fusion by CIViC, with gene identifiers per the VICC Fusion representation recommendation. CIViC did not provide identifiers for the genes, so HGNC identifiers were used.

• description: “An optional field to describe v::NTRK1(hgnc:8031)”, a placeholder since CIViC does not provide a longform description for this fusion.

• aliases: CIViC does not provide aliases for this fusion, so v::NTRK1 and NTRK1 fusion were added as examples.

• extensions: A “Known Gene Elements” extension captures a ConceptSet of known possible fusion partners from COSMIC Fusion data, listing LMNA, TFG, TP53, TPM3, and TPR with an OR membership operator.

• mappings: No mappings are included in this example.

Constraints

Adjacency Constraint: The adjoinedElements array specifies an UnspecifiedElement for the uncharacterized fusion partner and NTRK1 (hgnc:8031) as a mappable concept for the known partner. The orderKnown field is set to false to reflect that the 5’-to-3’ orientation between the partners has not been established.

Members

This example does not include members.

Full example: JSON

{
  "id": "civic.fid:62026",
  "type": "CategoricalVariant",
  "name": "v::NTRK1(hgnc:8031)",
  "description": "An optional field to describe v::NTRK1(hgnc:8031).",
  "aliases": [
    "v::NTRK1",
    "NTRK1 fusion"
  ],
  "constraints": [
    {
      "type": "AdjacencyConstraint",
      "orderKnown": false,
      "adjoinedElements": [
        {
          "type": "UnspecifiedElement"
        },
        {
          "id": "hgnc:8031",
          "conceptType": "Gene",
          "name": "NTRK1",
          "primaryCoding": {
            "id": "hgnc:8031",
            "name": "NTRK1",
            "system": "https://genenames.org",
            "code": "HGNC:8031",
            "iris": [
              "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:7230"
            ]
          }
        }
      ]
    }
  ],
  "extensions": [
    {
      "name": "Known Gene Elements",
      "description": "Known gene elements that may satisfy this Categorical Variant. Please specify if this array is exhaustive or non-exhaustive, and if it is subject to change.",
      "value": {
        "type": "ConceptSet",
        "membershipOperator": "OR",
        "concepts": [
          {
            "id": "hgnc:6636",
            "conceptType": "Gene",
            "name": "LMNA",
            "primaryCoding": {
              "id": "hgnc:6636",
              "name": "LMNA",
              "system": "https://genenames.org",
              "code": "HGNC:6636",
              "iris": [
                "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:6636"
              ]
            }
          },
          {
            "id": "hgnc:11758",
            "conceptType": "Gene",
            "name": "TFG",
            "primaryCoding": {
              "id": "hgnc:11758",
              "name": "TFG",
              "system": "https://genenames.org",
              "code": "HGNC:11758",
              "iris": [
                "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11758"
              ]
            }
          },
          {
            "id": "hgnc:11998",
            "conceptType": "Gene",
            "name": "TP53",
            "primaryCoding": {
              "id": "hgnc:11998",
              "name": "TP53",
              "system": "https://genenames.org",
              "code": "HGNC:11998",
              "iris": [
                "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998"
              ]
            }
          },
          {
            "id": "hgnc:12012",
            "conceptType": "Gene",
            "name": "TPM3",
            "primaryCoding": {
              "id": "hgnc:12012",
              "name": "TPM3",
              "system": "https://genenames.org",
              "code": "HGNC:12012",
              "iris": [
                "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:12012"
              ]
            }
          },
          {
            "id": "hgnc:12017",
            "conceptType": "Gene",
            "name": "TPR",
            "primaryCoding": {
              "id": "hgnc:12017",
              "name": "TPR",
              "system": "https://genenames.org",
              "code": "HGNC:12017",
              "iris": [
                "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:12017"
              ]
            }
          }
        ]
      }
    }
  ]
}

Full example: YAML