Enum: G2PConfidenceCategory

The level of confidence that a gene-disease association is real, as asserted by G2P curators. G2P uses the GenCC gene-disease validity classification terms. Operationally several groups use definitive, strong and moderate for clinical reporting; limited, disputed and refuted are not used for clinical reporting. GenCC classification identifiers are recorded in the gencc_classification_id annotation rather than as meaning:, because the GENCC prefix is not registered in bioregistry, OLS or the OBO PURL system and so cannot be resolved; the identifiers were taken from GenCC's own submissions export.

URI: valuesets:G2PConfidenceCategory

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Permissible Values

Value	Title	Description	Clinical Reporting	Gencc Classification Id
DEFINITIVE	definitive	The role of this gene in this particular disease has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time (at least 2 independent publication over 3 years' time). No convincing evidence has emerged that contradicts the role of the gene in the specified disease. (previously labelled as confirmed) The strength of evidence within publications as well as their number and publication dates is taken into account. In practice, this usually means at least 4 publications over 5 years. Typically this will also include convincing bioinformatic or functional evidence of causation, making it very unlikely that this gene-disease association would ever be refuted.	true	GENCC:100001
STRONG	strong	The role of this gene as a monogenic cause of disease has been repeatedly and independently demonstrated providing very strong convincing evidence in humans and no conflicting evidence for this gene's role in this disease. (previously labelled as probable).	true	GENCC:100002
MODERATE	moderate	There is moderate evidence in humans to support a casual role for this gene in this disease with no contradictory evidence. The body of evidence is not large (e.g possibly only one key paper) but appears convincing enough that the gene-disease pair is likely to be validated with additional evidence in the near future.	true	GENCC:100003
LIMITED	limited	Little human evidence exists to support a casual role for this gene in this disease, but not all evidence has been refuted. For example, there may be a collection of rare missense variants in humans but without convincing functional impact, segregration data that could either arise by chance (e.g across one or two meioses) or does not implicate a single gene, or functional data without direct recapitulation of the phenotype. Overall, the body of evidence does not meet contemporary criteria for claiming a valid association with disease. The majority are probably false associations. (previously labelled as possible).	false	GENCC:100004
DISPUTED	disputed	Although evidence has been reported, other evidence of equal weight disputes the claim.	false	GENCC:100005
REFUTED	refuted	There has been an assertion of a gene-disease association in the literature, but new valid evidence has arisen that refutes the entire original body of evidence.	false	GENCC:100006

Slots

Name	Description
g2p_confidence	The G2P confidence category assigned to a gene-disease association

Identifier and Mapping Information

Annotations

property	value
stewards	https://www.ebi.ac.uk/gene2phenotype
publishers	https://www.ebi.ac.uk/gene2phenotype
source	https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section
standard	GenCC gene-disease validity classification

Schema Source

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

LinkML Source

name: G2PConfidenceCategory
instantiates:
- valuesets_meta:ValueSetEnumDefinition
annotations:
  stewards:
    tag: stewards
    value: https://www.ebi.ac.uk/gene2phenotype
  publishers:
    tag: publishers
    value: https://www.ebi.ac.uk/gene2phenotype
  source:
    tag: source
    value: https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section
  standard:
    tag: standard
    value: GenCC gene-disease validity classification
description: The level of confidence that a gene-disease association is real, as asserted
  by G2P curators. G2P uses the GenCC gene-disease validity classification terms.
  Operationally several groups use definitive, strong and moderate for clinical reporting;
  limited, disputed and refuted are not used for clinical reporting. GenCC classification
  identifiers are recorded in the gencc_classification_id annotation rather than as
  meaning:, because the GENCC prefix is not registered in bioregistry, OLS or the
  OBO PURL system and so cannot be resolved; the identifiers were taken from GenCC's
  own submissions export.
title: G2P Confidence Category
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: STANDARD
rank: 1000
permissible_values:
  DEFINITIVE:
    text: DEFINITIVE
    description: The role of this gene in this particular disease has been repeatedly
      demonstrated in both the research and clinical diagnostic settings, and has
      been upheld over time (at least 2 independent publication over 3 years' time).
      No convincing evidence has emerged that contradicts the role of the gene in
      the specified disease. (previously labelled as confirmed) The strength of evidence
      within publications as well as their number and publication dates is taken into
      account. In practice, this usually means at least 4 publications over 5 years.
      Typically this will also include convincing bioinformatic or functional evidence
      of causation, making it very unlikely that this gene-disease association would
      ever be refuted.
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100001
      clinical_reporting:
        tag: clinical_reporting
        value: 'true'
    title: definitive
    aliases:
    - confirmed
  STRONG:
    text: STRONG
    description: The role of this gene as a monogenic cause of disease has been repeatedly
      and independently demonstrated providing very strong convincing evidence in
      humans and no conflicting evidence for this gene's role in this disease. (previously
      labelled as probable).
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100002
      clinical_reporting:
        tag: clinical_reporting
        value: 'true'
    title: strong
    aliases:
    - probable
  MODERATE:
    text: MODERATE
    description: There is moderate evidence in humans to support a casual role for
      this gene in this disease with no contradictory evidence. The body of evidence
      is not large (e.g possibly only one key paper) but appears convincing enough
      that the gene-disease pair is likely to be validated with additional evidence
      in the near future.
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100003
      clinical_reporting:
        tag: clinical_reporting
        value: 'true'
    title: moderate
  LIMITED:
    text: LIMITED
    description: Little human evidence exists to support a casual role for this gene
      in this disease, but not all evidence has been refuted. For example, there may
      be a collection of rare missense variants in humans but without convincing functional
      impact, segregration data that could either arise by chance (e.g across one
      or two meioses) or does not implicate a single gene, or functional data without
      direct recapitulation of the phenotype. Overall, the body of evidence does not
      meet contemporary criteria for claiming a valid association with disease. The
      majority are probably false associations. (previously labelled as possible).
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100004
      clinical_reporting:
        tag: clinical_reporting
        value: 'false'
    title: limited
    aliases:
    - possible
  DISPUTED:
    text: DISPUTED
    description: Although evidence has been reported, other evidence of equal weight
      disputes the claim.
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100005
      clinical_reporting:
        tag: clinical_reporting
        value: 'false'
    title: disputed
  REFUTED:
    text: REFUTED
    description: There has been an assertion of a gene-disease association in the
      literature, but new valid evidence has arisen that refutes the entire original
      body of evidence.
    annotations:
      gencc_classification_id:
        tag: gencc_classification_id
        value: GENCC:100006
      clinical_reporting:
        tag: clinical_reporting
        value: 'false'
    title: refuted