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Class: VariantPopulationEffect

A finding that a variant's effect differs, or was tested and found not to differ, in a named human population: its classification, penetrance, severity, phenotype spectrum, or frequency there. The population is recorded in the source's own words (population) and optionally bound to HANCESTRO (ancestry_terms), with ancestry_basis saying whether the source defined the group by self-report, genetic inference, or geography.

URI: dismech:class/VariantPopulationEffect

 classDiagram
    class VariantPopulationEffect
    click VariantPopulationEffect href "../../classes/VariantPopulationEffect/"
      VariantPopulationEffect : allele_frequency

      VariantPopulationEffect : ancestry_basis





        VariantPopulationEffect --> "0..1" AncestryBasisEnum : ancestry_basis
        click AncestryBasisEnum href "../../enums/AncestryBasisEnum/"



      VariantPopulationEffect : ancestry_terms





        VariantPopulationEffect --> "*" AncestryDescriptor : ancestry_terms
        click AncestryDescriptor href "../../classes/AncestryDescriptor/"



      VariantPopulationEffect : clinical_significance





        VariantPopulationEffect --> "0..1" ClinicalSignificanceEnum : clinical_significance
        click ClinicalSignificanceEnum href "../../enums/ClinicalSignificanceEnum/"



      VariantPopulationEffect : cohort_size

      VariantPopulationEffect : comparator_stratum

      VariantPopulationEffect : description

      VariantPopulationEffect : effect_differences





        VariantPopulationEffect --> "* _recommended_" PopulationEffectDifferenceEnum : effect_differences
        click PopulationEffectDifferenceEnum href "../../enums/PopulationEffectDifferenceEnum/"



      VariantPopulationEffect : evidence





        VariantPopulationEffect --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../../classes/EvidenceItem/"



      VariantPopulationEffect : notes

      VariantPopulationEffect : penetrance





        VariantPopulationEffect --> "0..1" PenetranceEnum : penetrance
        click PenetranceEnum href "../../enums/PenetranceEnum/"



      VariantPopulationEffect : penetrance_percentage

      VariantPopulationEffect : population

Slots

Name Cardinality and Range Description Inheritance
population 1
String		 The population in the source's own words (for example "Japanese FMF patients"... direct
ancestry_terms *
AncestryDescriptor		 HANCESTRO terms for the population, when the source supports a binding direct
ancestry_basis 0..1
AncestryBasisEnum		 How the source defined membership of the population direct
comparator_stratum 0..1
String		 The population the effect is compared with, in the source's own words (for ex... direct
effect_differences * recommended
PopulationEffectDifferenceEnum		 Which aspects of the variant's effect the source reports as differing in this... direct
clinical_significance 0..1
ClinicalSignificanceEnum		 direct
penetrance 0..1
PenetranceEnum		 Penetrance classification for this variant in this population direct
penetrance_percentage 0..1
FrequencyQuantity		 Estimated penetrance percentage or range (e direct
allele_frequency 0..1
Float		 Allele frequency of the variant in the population, as a proportion between 0 ... direct
cohort_size 0..1
Integer		 Number of patients or carriers the population-specific finding was computed f... direct
description 0..1
String		 direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Variant population_effects range VariantPopulationEffect

Comments

  • Record only what the source states. Do not set clinical_significance or effect_differences from your own comparison of two allele frequencies or two cohorts; a population difference must be reported by the source.
  • clinical_significance here is the classification the source gives for this population. It does not replace the variant-level clinical_significance, which remains the overall call.
  • A difference in response to treatment by ancestry belongs on the treatment's effect_modifiers (effect_modifier_type ANCESTRY), not here.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self dismech:VariantPopulationEffect
native dismech:VariantPopulationEffect

LinkML Source

Direct

name: VariantPopulationEffect
description: 'A finding that a variant''s effect differs, or was tested and found
  not to differ, in a named human population: its classification, penetrance, severity,
  phenotype spectrum, or frequency there. The population is recorded in the source''s
  own words (population) and optionally bound to HANCESTRO (ancestry_terms), with
  ancestry_basis saying whether the source defined the group by self-report, genetic
  inference, or geography.'
comments:
- Record only what the source states. Do not set clinical_significance or effect_differences
  from your own comparison of two allele frequencies or two cohorts; a population
  difference must be reported by the source.
- clinical_significance here is the classification the source gives for this population.
  It does not replace the variant-level clinical_significance, which remains the overall
  call.
- A difference in response to treatment by ancestry belongs on the treatment's effect_modifiers
  (effect_modifier_type ANCESTRY), not here.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- population
- ancestry_terms
- ancestry_basis
- comparator_stratum
- effect_differences
- clinical_significance
- penetrance
- penetrance_percentage
- allele_frequency
- cohort_size
- description
- evidence
- notes
slot_usage:
  population:
    name: population
    description: The population in the source's own words (for example "Japanese FMF
      patients", "Singaporean Chinese"). Kept even when ancestry_terms is bound, because
      it is the record of what the study said.
    required: true
  comparator_stratum:
    name: comparator_stratum
    description: The population the effect is compared with, in the source's own words
      (for example "Eastern Mediterranean populations"). Omit when the source reports
      the population alone.
  effect_differences:
    name: effect_differences
    recommended: true
  evidence:
    name: evidence
    recommended: true
  penetrance:
    name: penetrance
    description: Penetrance classification for this variant in this population.
  cohort_size:
    name: cohort_size
    description: Number of patients or carriers the population-specific finding was
      computed from, when reported.

Induced

name: VariantPopulationEffect
description: 'A finding that a variant''s effect differs, or was tested and found
  not to differ, in a named human population: its classification, penetrance, severity,
  phenotype spectrum, or frequency there. The population is recorded in the source''s
  own words (population) and optionally bound to HANCESTRO (ancestry_terms), with
  ancestry_basis saying whether the source defined the group by self-report, genetic
  inference, or geography.'
comments:
- Record only what the source states. Do not set clinical_significance or effect_differences
  from your own comparison of two allele frequencies or two cohorts; a population
  difference must be reported by the source.
- clinical_significance here is the classification the source gives for this population.
  It does not replace the variant-level clinical_significance, which remains the overall
  call.
- A difference in response to treatment by ancestry belongs on the treatment's effect_modifiers
  (effect_modifier_type ANCESTRY), not here.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  population:
    name: population
    description: The population in the source's own words (for example "Japanese FMF
      patients", "Singaporean Chinese"). Kept even when ancestry_terms is bound, because
      it is the record of what the study said.
    required: true
  comparator_stratum:
    name: comparator_stratum
    description: The population the effect is compared with, in the source's own words
      (for example "Eastern Mediterranean populations"). Omit when the source reports
      the population alone.
  effect_differences:
    name: effect_differences
    recommended: true
  evidence:
    name: evidence
    recommended: true
  penetrance:
    name: penetrance
    description: Penetrance classification for this variant in this population.
  cohort_size:
    name: cohort_size
    description: Number of patients or carriers the population-specific finding was
      computed from, when reported.
attributes:
  population:
    name: population
    description: The population in the source's own words (for example "Japanese FMF
      patients", "Singaporean Chinese"). Kept even when ancestry_terms is bound, because
      it is the record of what the study said.
    examples:
    - value: Global
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: population
    owner: VariantPopulationEffect
    domain_of:
    - PhenotypeContext
    - ReferenceRange
    - Prevalence
    - GeneCaseFraction
    - VariantPopulationEffect
    - AssociationSignal
    range: string
    required: true
  ancestry_terms:
    name: ancestry_terms
    description: 'HANCESTRO terms for the population, when the source supports a binding.
      Optional and multivalued: an admixed or multi-site cohort may take more than
      one. Bind what the source reports, at the level it reports it; do not bind a
      reference-panel term (1KGP, HGDP, SGDP) unless the data came from that panel.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: ancestry_terms
    owner: VariantPopulationEffect
    domain_of:
    - VariantPopulationEffect
    range: AncestryDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  ancestry_basis:
    name: ancestry_basis
    description: How the source defined membership of the population.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: ancestry_basis
    owner: VariantPopulationEffect
    domain_of:
    - VariantPopulationEffect
    range: AncestryBasisEnum
  comparator_stratum:
    name: comparator_stratum
    description: The population the effect is compared with, in the source's own words
      (for example "Eastern Mediterranean populations"). Omit when the source reports
      the population alone.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: comparator_stratum
    owner: VariantPopulationEffect
    domain_of:
    - TreatmentEffectModifier
    - VariantPopulationEffect
    range: string
  effect_differences:
    name: effect_differences
    description: Which aspects of the variant's effect the source reports as differing
      in this population. NO_DIFFERENCE records a tested null.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: effect_differences
    owner: VariantPopulationEffect
    domain_of:
    - VariantPopulationEffect
    range: PopulationEffectDifferenceEnum
    recommended: true
    multivalued: true
  clinical_significance:
    name: clinical_significance
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: clinical_significance
    owner: VariantPopulationEffect
    domain_of:
    - Variant
    - VariantPopulationEffect
    range: ClinicalSignificanceEnum
  penetrance:
    name: penetrance
    description: Penetrance classification for this variant in this population.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: penetrance
    owner: VariantPopulationEffect
    domain_of:
    - Inheritance
    - VariantPopulationEffect
    range: PenetranceEnum
  penetrance_percentage:
    name: penetrance_percentage
    description: Estimated penetrance percentage or range (e.g., 80-90)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: penetrance_percentage
    owner: VariantPopulationEffect
    domain_of:
    - Inheritance
    - VariantPopulationEffect
    range: FrequencyQuantity
  allele_frequency:
    name: allele_frequency
    description: Allele frequency of the variant in the population, as a proportion
      between 0 and 1, copied from the source. Say in notes whether it was measured
      in patients, carriers, or the general population.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: allele_frequency
    owner: VariantPopulationEffect
    domain_of:
    - VariantPopulationEffect
    range: float
    minimum_value: 0
    maximum_value: 1
  cohort_size:
    name: cohort_size
    description: Number of patients or carriers the population-specific finding was
      computed from, when reported.
    examples:
    - value: '61'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cohort_size
    owner: VariantPopulationEffect
    domain_of:
    - GeneCaseFraction
    - VariantPopulationEffect
    range: integer
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: VariantPopulationEffect
    domain_of:
    - Descriptor
    - DietaryModification
    - GenomicRegion
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: VariantPopulationEffect
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  notes:
    name: notes
    examples:
    - value: Contagious stage where symptoms appear and the bacteria can be spread
        to others.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: notes
    owner: VariantPopulationEffect
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassification
    - GeneClassificationCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - Transmission
    - Diagnosis
    - VariantPopulationEffect
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string