Enum: ACMGPathogenicityEnum

ACMG/AMP variant pathogenicity classification for clinical genetics

Permissible Values

Value	Title	Meaning	Description	Abbreviation	Clinical Significance	Note	Probability
PATHOGENIC	Pathogenic Variant	NCIT:C168799	Pathogenic variant	P	Disease-causing
LIKELY_PATHOGENIC	Likely Pathogenic Variant	NCIT:C168800	Likely pathogenic variant	LP			>90% certain
UNCERTAIN_SIGNIFICANCE	Variant of Unknown Significance	NCIT:C94187	Variant of uncertain significance	VUS		Insufficient evidence
LIKELY_BENIGN	Variant Likely Benign	NCIT:C168801	Likely benign variant	LB			>90% certain benign
BENIGN	Variant Benign	NCIT:C168802	Benign variant	B	Not disease-causing

Slots

Name	Description
acmg_pathogenicity	ACMG/AMP variant pathogenicity classification for clinical genetics

Identifier and Mapping Information

Annotations

property	value
stewards	https://phenopackets.org
publishers	https://ga4gh.org

Schema Source

from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: ACMGPathogenicityEnum
instantiates:
- valuesets_meta:ValueSetEnumDefinition
annotations:
  stewards:
    tag: stewards
    value: https://phenopackets.org
  publishers:
    tag: publishers
    value: https://ga4gh.org
description: ACMG/AMP variant pathogenicity classification for clinical genetics
title: ACMG Pathogenicity
from_schema: https://w3id.org/linkml/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: STANDARD
rank: 1000
permissible_values:
  PATHOGENIC:
    text: PATHOGENIC
    description: Pathogenic variant
    meaning: NCIT:C168799
    annotations:
      abbreviation:
        tag: abbreviation
        value: P
      clinical_significance:
        tag: clinical_significance
        value: Disease-causing
    title: Pathogenic Variant
  LIKELY_PATHOGENIC:
    text: LIKELY_PATHOGENIC
    description: Likely pathogenic variant
    meaning: NCIT:C168800
    annotations:
      abbreviation:
        tag: abbreviation
        value: LP
      probability:
        tag: probability
        value: '>90% certain'
    title: Likely Pathogenic Variant
  UNCERTAIN_SIGNIFICANCE:
    text: UNCERTAIN_SIGNIFICANCE
    description: Variant of uncertain significance
    meaning: NCIT:C94187
    annotations:
      abbreviation:
        tag: abbreviation
        value: VUS
      note:
        tag: note
        value: Insufficient evidence
    title: Variant of Unknown Significance
  LIKELY_BENIGN:
    text: LIKELY_BENIGN
    description: Likely benign variant
    meaning: NCIT:C168801
    annotations:
      abbreviation:
        tag: abbreviation
        value: LB
      probability:
        tag: probability
        value: '>90% certain benign'
    title: Variant Likely Benign
  BENIGN:
    text: BENIGN
    description: Benign variant
    meaning: NCIT:C168802
    annotations:
      abbreviation:
        tag: abbreviation
        value: B
      clinical_significance:
        tag: clinical_significance
        value: Not disease-causing
    title: Variant Benign