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Enum: VariantTypeEnum

Physical sequence alteration, independently of genomic location or functional consequence. Human-readable values map to Sequence Ontology. This is an optional classification alongside the legacy free-text type; it is not an exhaustive vocabulary for complex rearrangements.

URI: dismech:enum/VariantTypeEnum

Permissible Values

Value Meaning Description
single nucleotide variant SO:0001483 SNV
deletion SO:0000159 deletion
insertion SO:0000667 insertion
duplication SO:1000035 duplication
inversion SO:1000036 inversion
translocation SO:0000199 translocation
copy number variation SO:0001019 copy_number_variation
short tandem repeat expansion SO:0002162 short_tandem_repeat_expansion

Slots

Name Description
variant_type Optional controlled physical variant class

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: VariantTypeEnum
description: Physical sequence alteration, independently of genomic location or functional
  consequence. Human-readable values map to Sequence Ontology. This is an optional
  classification alongside the legacy free-text type; it is not an exhaustive vocabulary
  for complex rearrangements.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
permissible_values:
  single nucleotide variant:
    text: single nucleotide variant
    description: SNV
    meaning: SO:0001483
    notes:
    - A single-nucleotide change; does not assert population frequency as SNP would.
  deletion:
    text: deletion
    description: deletion
    meaning: SO:0000159
  insertion:
    text: insertion
    description: insertion
    meaning: SO:0000667
  duplication:
    text: duplication
    description: duplication
    meaning: SO:1000035
  inversion:
    text: inversion
    description: inversion
    meaning: SO:1000036
  translocation:
    text: translocation
    description: translocation
    meaning: SO:0000199
  copy number variation:
    text: copy number variation
    description: copy_number_variation
    meaning: SO:0001019
    notes:
    - Use deletion or duplication when the physical alteration is known.
  short tandem repeat expansion:
    text: short tandem repeat expansion
    description: short_tandem_repeat_expansion
    meaning: SO:0002162
    notes:
    - Do not use for repeat expansions outside the short tandem repeat class.