Enum: GenomicContextEnum

Genomic features overlapped by a variant, independently of its functional effect. Values describe sequence features, not variant consequences. Contexts may overlap and are relative to the relevant gene or transcript; record those details in the variant description.

URI: dismech:enum/GenomicContextEnum

Permissible Values

Value	Meaning	Description
coding sequence	SO:0000316	CDS
intron	SO:0000188	intron
5' UTR	SO:0000204	five_prime_UTR
3' UTR	SO:0000205	three_prime_UTR
noncoding exon	SO:0000198	noncoding_exon
intergenic region	SO:0000605	intergenic_region

Slots

Name	Description
genomic_contexts	Sequence features overlapped by the variant

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch-initiative/dismech

LinkML Source

name: GenomicContextEnum
description: Genomic features overlapped by a variant, independently of its functional
  effect. Values describe sequence features, not variant consequences. Contexts may
  overlap and are relative to the relevant gene or transcript; record those details
  in the variant description.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
permissible_values:
  coding sequence:
    text: coding sequence
    description: CDS
    meaning: SO:0000316
  intron:
    text: intron
    description: intron
    meaning: SO:0000188
  5' UTR:
    text: 5' UTR
    description: five_prime_UTR
    meaning: SO:0000204
  3' UTR:
    text: 3' UTR
    description: three_prime_UTR
    meaning: SO:0000205
  noncoding exon:
    text: noncoding exon
    description: noncoding_exon
    meaning: SO:0000198
    notes:
    - An entire exon without codons; use a UTR value for the untranslated part of
      an otherwise coding exon.
  intergenic region:
    text: intergenic region
    description: intergenic_region
    meaning: SO:0000605