NRAS functionally normal variants

Source

CIViC molecular profile id 4428: NRAS Wild type

Recipes that this example satisfies

Function Variant

Properties

id: civic.mpid:4428: CIViC Molecular Profile ID, where mpid stands for Molecular Profile ID, derived from the Molecular Profile 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: NRAS functionally normal variants: Chosen to represent the set of NRAS variants that are likely neutral rather than using CIViC’s “Wild type” framing.
description: A brief placeholder note.: This field was populated with an example value because CIViC does not provide a longform description.
aliases: null: No aliases included in this example.
extensions: null: No extensions included.
mappings: null: No mappings included.

Constraints

Feature Context Constraint: The featureContext is a Mappable Concept for NRAS (hgnc:7989), with a primaryCoding linking to its HGNC entry.
Function Constraint: The functionConsequence is a Mappable Concept for functionally normal (SO:0002219), with a primaryCoding linking to the Sequence Ontology term functionally_normal.

Members

The members field includes one VRS Allele object generated using the VICC Variation Normalizer for NM_002524.5(NRAS):c.170A>C (p.D57A), a variant categorized as Likely Neutral by OncoKB, on the MANE Select coding transcript for NRAS (refseq:NM_002524.5).

Full example: JSON

{
  "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"
      }
    }
  ]
}

Full example: YAML

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