Data Model

The ClinVar-GKS release file organizes data into bundle sections, each containing objects of a specific class. These classes form a directed graph of relationships — variants reference alleles, alleles reference locations, statements reference propositions, and so on.

This page provides a visual overview of how the classes relate to each other, with links to detailed documentation for each class.

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Class Relationship Diagram

The diagram below shows how the bundle classes relate to each other in a UML-style view. Each class shows its key attributes. Lines indicate reference relationships — navigable from the class with the arrow. Multiplicity is shown on each end.

classDiagram
    direction TB

    namespace Variation {
        class SequenceReference {
            refgetAccession : string
            residueAlphabet : string
            molecularType : string
            extensions : Extension[0..*]
        }
        class Location {
            id : ga4gh:SL.digest
            start : integer
            end : integer
        }
        class Allele {
            id : ga4gh:VA.digest
            state : object
            expressions : Expression[0..*]
        }
        class Gene {
            id : ncbigene:id
            conceptType : gene
            name : string
            primaryCoding : Coding
            mappings : Mapping[0..*]
        }
        class CategoricalVariant {
            id : clinvar:id
            type : string
            name : string
            constraints : Constraint[0..*]
            mappings : Mapping[0..*]
            extensions : Extension[0..*]
        }
    }

    namespace Supporting {
        class Condition {
            id : clinvar.trait:id
            name : string
            primaryCoding : Coding
            mappings : Mapping[0..*]
        }
        class ConditionSet {
            id : clinvar.traitset:id
            operator : AND | OR
        }
        class Submitter {
            id : clinvar.submitter:id
            name : string
        }
        class Proposition {
            id : string
            type : string
            predicate : string
            geneContextQualifier : Concept[0..1]
            modeOfInheritanceQualifier : Concept[0..1]
            penetranceQualifier : Concept[0..1]
        }
    }

    namespace Statements {
        class ScvStatement {
            id : clinvar.submission:id.ver
            type : Statement
            classification : MappableConcept
            strength : MappableConcept
            direction : string
            confidence : Concept
            contributions : Contribution[1..*]
            specifiedBy : Method[0..1]
            reportedIn : Publication[0..*]
            extensions : Extension[0..*]
        }
        class VcvStatement {
            id : VCV.ver-group-PROP-level
            type : Statement
            classification : MappableConcept
            strength : MappableConcept
            direction : string
            confidence : Concept
            extensions : Extension[0..*]
        }
        class RcvStatement {
            id : RCV.ver-group-PROP-level
            type : Statement
            classification : MappableConcept
            strength : MappableConcept
            direction : string
            confidence : Concept
            extensions : Extension[0..*]
        }
        class EvidenceLine {
            type : EvidenceLine
            directionOfEvidenceProvided : string
            strengthOfEvidenceProvided : MappableConcept
        }
    }

    %% Variation relationships
    Location "1" --> "1" SequenceReference : sequenceReference
    Allele "1" --> "1" Location : location
    CategoricalVariant "*" --> "0..*" Allele : members
    CategoricalVariant "*" ..> "0..*" Gene : extensions.clinvarGeneList

    %% Supporting relationships
    ConditionSet "1" --> "1..*" Condition : members
    Proposition "*" --> "1" CategoricalVariant : subjectVariant
    Proposition "*" --> "0..1" Condition : objectCondition
    Proposition "*" --> "0..1" ConditionSet : objectCondition

    %% Statement → Proposition
    ScvStatement "1" --> "1" Proposition : proposition
    VcvStatement "1" --> "1" Proposition : proposition
    RcvStatement "1" --> "1" Proposition : proposition

    %% Statement → Submitter
    ScvStatement "*" --> "1..*" Submitter : contributions

    %% Evidence lines
    ScvStatement "1" --> "0..*" EvidenceLine : hasEvidenceLines
    VcvStatement "1" --> "1..*" EvidenceLine : hasEvidenceLines
    RcvStatement "1" --> "1..*" EvidenceLine : hasEvidenceLines

    %% Evidence items (what evidence lines reference)
    EvidenceLine "*" --> "1..*" ScvStatement : evidenceItems
    EvidenceLine "*" ..> "0..*" VcvStatement : evidenceItems
    EvidenceLine "*" ..> "0..*" RcvStatement : evidenceItems

Reading the diagram:

• Solid lines are primary associations — always present when the parent object exists
• Dashed lines are optional or conditional associations (e.g., gene list from extensions, VCV/RCV self-referencing through evidence lines)
• Multiplicity on each end indicates cardinality (e.g., 1 = exactly one, 0..* = zero or more, 1..* = one or more)
• Labels on lines show the field name or JSON pointer path used for the reference

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Variation Classes

These classes represent the variant and its genomic context. VRS types (SequenceReference, Location, Allele) use their upstream GA4GH schemas directly. ClinVar-specific profiles are documented under Variations.

Class	Bundle Section	Key Pattern	Description
SequenceReference	sequenceReference	SQ.{digest}	Reference sequence with refget accession, molecule type, and assembly
Location	location	ga4gh:SL.{digest}	Position or range on a sequence reference
Allele	allele	ga4gh:VA.{digest}	Specific sequence change at a location
Gene	gene	ncbigene:{id}	Gene MappableConcept with NCBI Gene primaryCoding and HGNC mapping
ClinvarCategoricalVariant	variation	clinvar:{id}	ClinVar variation with Cat-VRS representation and extensions

See Variations for the full variant type hierarchy and extension documentation.

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Supporting Classes

These classes represent the conditions, submitters, and propositions that support classification statements. Conditions and submitters use upstream GA4GH types. ClinVar-specific proposition types are documented under Propositions.

Class	Bundle Section	Key Pattern	Description
Condition	condition	clinvar.trait:{id}	Disease or phenotype with MedGen coding and cross-references
ConditionSet	conditionSet	clinvar.traitset:{id}	Grouping of conditions with AND/OR membership operator
Submitter	submitter	clinvar.submitter:{id}	Submitting organization
ClinvarProposition	proposition	{scv_id}-{CODE}	Classification proposition (12 types)

See Propositions for the full type/code/predicate reference.

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Statement Classes

These classes represent classification statements at different levels of aggregation. All are profiles of the VA-Spec Statement type documented under Statements.

Class	Bundle Section	Key Pattern	Description
ClinvarScvStatement	scv	clinvar.submission:{id}.{ver}	Submitted classification
ClinvarVcvStatement	vcv	{vcv}-{group}-{prop}-{level}	Variant-level aggregate
ClinvarRcvStatement	rcv	{rcv}-{group}-{prop}-{level}	Condition-level aggregate
ClinvarSomaticEvidenceLine	evidenceLine	{scv_id}.{ver} / {agg_id}.contributing	Evidence line referenced via hasEvidenceLines

See Statements for the aggregation structure and Evidence Lines for the somatic tier mapping.