cat-vrs/examples/yaml/adjacencyFusion-ex1.yaml at v1 · ga4gh/cat-vrs · GitHub

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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:
      - type: MappableConcept
        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
      - type: MappableConcept
        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