BCR(ncbi:613)::ABL1(ncbi:25)

Source: CIViC variant id 1: BCR::ABL1 Fusion

Recipes that this example satisfies: Gene Fusion

Attributes

• id: “civic.vid:1”, where vid stands for Variant ID, derived from the Variant ID contained within the CIViC URL for this genomic alteration.

• type: “CategoricalVariant”, as required by the specification.

• name: “BCR(ncbi:613)::ABL1(ncbi:25)”, which is the human-readable label given to the fusion by CIViC, with gene identifiers per the VICC Fusion representation recommendation. CIViC provided NCBI identifiers for both genes, so those were used.

• description: “An optional field to describe BCR::ABL1” was used as a placeholder since CIViC does not provide a longform description for this fusion.

• aliases: All aliases for BCR::ABL1 were provided as aliases, as provided by CIViC.

• extensions: The 5’ and 3’ Partner Representative Genomic Coordinates for BCR::ABL1, as provided by CIViC.

• mappings: No mappings are included in this example.

Constraints

Adjacency Constraint: Both BCR and ABL1 are modeled as mappable concepts within the adjoinedElements array, using the NCBI gene identifiers provided by CIViC (ncbi:613 for BCR and ncbi:25 for ABL1). The orderKnown field is set to true to indicate that the 5’-to-3’ orientation of the fusion partners is known.

Members

The members field includes a VRS Adjacency object representing the BCR::ABL1 gene fusion using illustrative transcript breakpoint coordinates. Specifically, it encodes NM_004327.4:r.1_3533::NM_005157.6:r.461_5766, using the MANE Select transcripts for BCR (NM_004327.4) and ABL1 (NM_005157.6).

Full example: JSON

{
  "id": "civic.vid:1",
  "type": "CategoricalVariant",
  "name": "BCR(ncbi:613)::ABL1(ncbi:25)",
  "description": "An optional field to describe BCR::ABL1",
  "aliases": [
    "BCR::ABL1",
    "t(9;22)(q34;q11)",
    "BCR-ABL1",
    "BCR--ABL1",
    "BCR-ABL",
    "BCR(hgnc:1014)::ABL1(hgnc:76)"
  ],
  "extensions": [
    {
      "name": "CIViC 5' Partner Representative Genomic Coordinates",
      "value": {
        "reference_build": "GRCh37",
        "transcript": "ENST00000305877.8",
        "ensembl_version": 75,
        "chromosome": "22",
        "start": 23522397,
        "end": 23632600
      }
    },
    {
      "name": "CIViC 3' Partner Representative Genomic Coordinates",
      "value": {
        "reference_build": "GRCh37",
        "transcript": "ENST00000318560.5",
        "ensembl_version": 75,
        "chromosome": "9",
        "start": 133729451,
        "end": 133763062
      }
    }
  ],
  "constraints": [
    {
      "type": "AdjacencyConstraint",
      "orderKnown": true,
      "adjoinedElements": [
        {
          "id": "ncbi:613",
          "conceptType": "Gene",
          "name": "BCR",
          "primaryCoding": {
            "id": "ncbi:613",
            "name": "BCR",
            "system": "https://www.ncbi.nlm.nih.gov/gene",
            "code": "613",
            "iris": [
              "https://www.ncbi.nlm.nih.gov/gene/613"
            ]
          }
        },
        {
          "id": "ncbi:25",
          "conceptType": "Gene",
          "name": "ABL1",
          "primaryCoding": {
            "id": "ncbi:25",
            "name": "ABL1",
            "system": "https://www.ncbi.nlm.nih.gov/gene",
            "code": "25",
            "iris": [
              "https://www.ncbi.nlm.nih.gov/gene/25"
            ]
          }
        }
      ]
    }
  ],
  "members": [
    {
      "id": "ga4gh:AJ.KMisuH8wK4gWBigo1o4DHarzi_Xm5g9f",
      "type": "Adjacency",
      "name": "NM_004327.4:r.1_3533::NM_005157.6:r.461_5766 gene fusion.",
      "description": "Example BCR::ABL1 gene fusion, NM_004327.4:r.1_3533::NM_005157.6:r.461_5766, using illustrative transcript breakpoint coordinates.",
      "digest": "KMisuH8wK4gWBigo1o4DHarzi_Xm5g9f",
      "adjoinedSequences": [
        {
          "id": "ga4gh:SL.SgudSwN0DssFbctqKs05wWDxBFJiFD4G",
          "type": "SequenceLocation",
          "digest": "SgudSwN0DssFbctqKs05wWDxBFJiFD4G",
          "sequenceReference": {
            "id": "refseq:NM_004327.4",
            "type": "SequenceReference",
            "name": "NM_004327.4",
            "description": "BCR MANE Select transcript.",
            "aliases": [
              "ensembl:ENST00000305877.13",
              "ga4gh:SQ.kpytJsXw3BwLC3oBSjHQS1kwxs4WO3I3"
            ],
            "refgetAccession": "SQ.kpytJsXw3BwLC3oBSjHQS1kwxs4WO3I3",
            "residueAlphabet": "na"
          },
          "end": 3533
        },
        {
          "id": "ga4gh:SL.vrnSNKA1YzeUjl5JlZ5wjHOTMKkXk_sQ",
          "type": "SequenceLocation",
          "digest": "vrnSNKA1YzeUjl5JlZ5wjHOTMKkXk_sQ",
          "sequenceReference": {
            "id": "refseq:NM_005157.6",
            "type": "SequenceReference",
            "name": "NM_005157.6",
            "description": "ABL1 MANE Select transcript.",
            "aliases": [
              "ensembl:ENST00000318560.6",
              "ga4gh:SQ.w8Qg3x-PQ2akJrJQeGEN-_eBUMo1H1CL"
            ],
            "refgetAccession": "SQ.w8Qg3x-PQ2akJrJQeGEN-_eBUMo1H1CL",
            "residueAlphabet": "na"
          },
          "start": 460
        }
      ]
    }
  ]
}

Full example: YAML