BCR(ncbi:613)::ABL1(ncbi:25)

Source

CIViC variant id 1: BCR::ABL1 Fusion

Recipes that this example satisfies

Gene Fusion

Properties

id: civic.vid:1: CIViC Variant ID, where vid stands for Variant ID, derived from the Variant ID contained within the CIViC URL for this genomic alteration.
type: CategoricalVariant: This value is required by the specification for all Categorical Variant objects.
name: BCR(ncbi:613)::ABL1(ncbi:25): 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 this Categorical Variant.: This field was populated with an example value because CIViC does not provide a longform description.
aliases: BCR::ABL1, t(9;22)(q34;q11), BCR-ABL1, BCR–ABL1, BCR-ABL, BCR(hgnc:1014)::ABL1(hgnc:76): All aliases, as provided by CIViC, were included.
extensions: CIViC 5’ and 3’ Partner Representative Genomic Coordinates for BCR::ABL1: CIViC provided these values within the variant object, so we included them here as extensions to because the data model does not explicitly support them.
mappings: null: No mappings included.

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 this Categorical Variant.",
  "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

id: civic.vid:1
type: CategoricalVariant
name: BCR(ncbi:613)::ABL1(ncbi:25)
description: An optional field to describe this Categorical Variant.
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