SCV Statements¶

Overview¶

The scv bundle section contains one record per ClinVar submission (SCV). Each record is a VA-Spec Statement that captures a submitter's interpretation of a variant — including the classification, evidence, condition, variant, and method.

SCV statements use #/ references to link to propositions, submitters, and conditions in their respective bundle sections rather than embedding full objects inline.

This section is produced by the SCV Statements procedure.

Record Structure¶

Each record is a VA-Spec Statement with the following top-level fields:

Field	Type	Description
`id`	string	SCV accession with version — `clinvar.submission:SCV000123456.1`
`type`	string	Always `Statement`
`proposition`	string	`#/proposition/{id}` reference to the classification proposition
`classification`	object	MappableConcept — the submitter's classification. See Classification
`strength`	object	MappableConcept — the evidence strength. See Strength
`direction`	string	Whether the evidence `supports`, `disputes`, or is `neutral` toward the proposition
`confidence`	object	Concept struct with `conceptType: "Confidence"` and `name` (the submission level label). See Confidence
`description`	string	Free-text interpretation summary (when provided by the submitter)
`contributions`	array	Submitter and date information with `#/submitter/` references. See Contributions
`specifiedBy`	object	The classification method/guideline used
`reportedIn`	array	Supporting publications (PubMed, DOI references)
`extensions`	array of Extension	ClinVar-specific metadata (0..*). See Extensions
`hasEvidenceLines`	array	Evidence lines for somatic clinical impact assertions. See Evidence Lines

Classification¶

The classification field is a MappableConcept with the submitted classification:

{
  "conceptType": "Classification",
  "name": "Pathogenic",
  "primaryCoding": {
    "code": "pathogenic",
    "system": "ACMG Guidelines, 2015"
  },
  "extensions": [
    {
      "name": "description",
      "value": "for Hemochromatosis\nClassification is based on the criteria provided submission\nMay 2021 by Victorian Clinical Genetics Services"
    }
  ]
}

The primaryCoding provides the machine-readable classification code and system from the clinvar_clinsig_types lookup table. The extensions array contains a human-readable description summarizing the condition, submission level, evaluation date, and submitter.

Strength¶

The strength field is a MappableConcept indicating the evidence strength:

{
  "conceptType": "Strength",
  "name": "Definitive",
  "primaryCoding": {
    "code": "definitive",
    "system": "ACMG Guidelines, 2015"
  }
}

The primaryCoding is present when the strength can be mapped to a specific code in the classification system.

Confidence¶

The confidence field is a Concept struct indicating the submission level:

{
  "conceptType": "Confidence",
  "name": "criteria provided"
}

Field	Type	Description
`conceptType`	string	Always `"Confidence"`
`name`	string	The submission level label (e.g., `criteria provided`, `practice guideline`, `expert panel`)

Contributions¶

The contributions array records the submitter and key dates. Each contribution references the submitter via #/submitter/:

[
  {
    "type": "Contribution",
    "contributor": "#/submitter/clinvar.submitter:500104",
    "date": "2022-12-24",
    "activityType": "submitted"
  },
  {
    "type": "Contribution",
    "contributor": "#/submitter/clinvar.submitter:500104",
    "date": "2022-12-24",
    "activityType": "created"
  },
  {
    "type": "Contribution",
    "contributor": "#/submitter/clinvar.submitter:500104",
    "date": "2021-05-06",
    "activityType": "evaluated"
  }
]

Proposition¶

SCV propositions are stored in the proposition bundle section, referenced by #/proposition/{id}. The proposition ID combines the SCV accession with an uppercase proposition type code:

SCV001234567-PATH

A resolved proposition contains:

Field	Type	Description
`id`	string	Proposition ID (e.g., `SCV001234567-PATH`)
`type`	string	Proposition type (e.g., `VariantPathogenicityProposition`)
`predicate`	string	The relationship asserted (e.g., `isCausalFor`)
`subjectVariant`	string	`#/variation/clinvar:{id}` reference
`objectCondition`	string	`#/condition/clinvar.trait:{id}` or `#/conditionSet/clinvar.traitset:{id}` reference
`geneContextQualifier`	object	Gene context with NCBI Gene and HGNC identifiers (when applicable)
`modeOfInheritanceQualifier`	object	Mode of inheritance with HPO coding (when submitted)
`penetranceQualifier`	object	Penetrance qualifier (for low-penetrance/risk factor classifications)

Proposition Types¶

Proposition Type	Code	Predicate	Description
`VariantPathogenicityProposition`	`PATH`	`isCausalFor`	Germline pathogenicity/benignity
`VariantOncogenicityProposition`	`ONCO`	`isOncogenicFor`	Oncogenicity
`VariantClinicalSignificanceProposition`	`SCI`	`isClinicallySignificantFor`	Somatic clinical impact
`ClinvarAssociationProposition`	`ASSOC`	`isAssociatedWith`	Association
`ClinvarRiskFactorProposition`	`RF`	`isRiskFactorFor`	Risk factor
`ClinvarDrugResponseProposition`	`DR`	`hasDrugResponseFor`	Drug response
`ClinvarProtectiveProposition`	`PROT`	`isProtectiveFor`	Protective
`ClinvarAffectsProposition`	`AFF`	`hasAffectFor`	Affects
`ClinvarConfersSensitivityProposition`	`CS`	`confersSensitivityFor`	Confers sensitivity
`ClinvarOtherProposition`	`OTH`	`isClinvarOtherAssociationFor`	Other
`ClinvarNotProvidedProposition`	`NP`	`hasNoProvidedClassificationFor`	Not provided
`ClinvarConflictingDataFromSubmitterProposition`	`CONF`	`isConflictingDataFromSubmittersFor`	Conflicting data

For somatic clinical impact, target propositions (evidence line propositions) use these codes: PROG (Prognostic), DIAG (Diagnostic), TR (Therapeutic Response).

See Propositions for the full profile documentation.

Evidence Lines¶

Evidence lines appear on somatic clinical impact (SCI) statements. Each evidence line carries a target proposition, direction, outcome, and condition extensions:

{
  "type": "EvidenceLine",
  "proposition": "#/proposition/SCV004565358-TR",
  "directionOfEvidenceProvided": "supports",
  "evidenceOutcome": {
    "conceptType": "Outcome",
    "name": "tier 1"
  },
  "extensions": [ ... ]
}

The evidenceOutcome is a MappableConcept with conceptType: "Outcome" indicating the tier classification for the target proposition.

Extensions¶

Extensions carry ClinVar-specific metadata not part of the GA4GH VA-Spec statement model. Each extension follows the GA4GH Extension structure: { "name": "<name>", "value": <value> }. Extensions appear at three structural levels — on the top-level Statement, on the classification object, and on proposition qualifier objects.

See SCV Extensions (Pipeline) for details on how these extensions are built during pipeline processing.

Statement Extensions¶

Extension Name	Value Type	Description
`clinvarScvId`	`string`	The ClinVar SCV accession without version (e.g., `SCV001571657`). Always present.
`clinvarScvVersion`	`string`	The version number of the SCV submission (e.g., `2`). Always present.
`submittedCondition`	SubmittedCondition	Submitted condition provenance with normalization details, trait mapping, and `#/condition/` references. Present when the SCV maps to a single condition.
`submittedConditionSet`	SubmittedConditionSet	Submitted condition set provenance with multiple condition concepts. Present when the SCV maps to multiple conditions.
`clinvarScvReviewStatus`	`string`	The ClinVar review status (e.g., `criteria provided, single submitter`). Present when the SCV has a review status.
`submittedScvClassification`	`string`	The original classification text submitted by the submitter, preserved when it differs from the normalized classification name.
`submittedScvLocalKey`	`string`	The unique local key provided by the submitter for this submission. Present only when the submitter provided a local key.
`submissionLevel`	`string`	The submission level code: `PG`, `EP`, `CP`, `NOCP`, `NOCL`, or `FLAG`. Present when the submission level can be determined.

Note

Only one of submittedCondition or submittedConditionSet is present per SCV — never both. The submittedScvClassification extension is omitted when the submitted classification matches the normalized label exactly.

Classification Extensions¶

Extensions on the classification MappableConcept within the Statement.

Extension Name	Value Type	Description
`description`	`string`	A formatted multi-line description summarizing the classification context: condition name, submission level, evaluation date, and submitter name. Always present.

The description template is: for <condition_name>\nClassification is based on the <submission_level_label> submission\n<evaluated_date> by <submitter_name>.

Qualifier Extensions¶

Extensions on proposition qualifier objects (geneContextQualifier, modeOfInheritanceQualifier, penetranceQualifier), preserving the original submitter-provided values.

Extension Name	Value Type	Description
`submittedGeneSymbols`	array of `string`	Gene symbols originally submitted by the submitter. Present on `geneContextQualifier` when the submitter provided gene information. May differ from the normalized gene symbol.
`submittedModeOfInheritance`	`string`	Mode of inheritance text as originally submitted. Present on all `modeOfInheritanceQualifier` objects. Preserved alongside the normalized HPO coding.
`submittedClassification`	`string`	Original submitted classification text that triggered the penetrance qualifier derivation. Present on all `penetranceQualifier` objects.

SubmittedCondition¶

The submittedCondition extension captures the provenance of how a single submitted condition was mapped to the normalized ClinVar trait. Present when the SCV maps to exactly one condition.

Field	Type	Description
`condition`	`string`	`#/condition/clinvar.trait:{id}` reference to the normalized condition in the bundle.
`conditionSet`	`string`	`#/conditionSet/clinvar.traitset:{id}` reference (present when the RCV trait set has one trait but the reference uses the set).
`id`	`string`	The submitted clinical assertion trait ID (e.g., `SCV002769510.0`).
`name`	`string`	The submitted condition name.
`type`	`string`	The submitted condition type (e.g., `Disease`, `Finding`).
`medgen_id`	`string`	The submitted or resolved MedGen concept ID.
`normalized_match`	`string`	`#/condition/` reference to the matched normalized trait.
`normalized_resolution`	`string`	The resolution method used to match the submitted condition (e.g., `tm reftype xref omim`, `random trait assignment`).
`xrefs`	array	Submitted cross-references with `code` and `system`.
`mapping`	object	The trait mapping entry used for resolution: `type`, `ref`, `value`.

SubmittedConditionSet¶

The submittedConditionSet extension captures provenance for multi-condition submissions. Present when the SCV maps to more than one condition.

Field	Type	Description
`conditionSet`	`string`	`#/conditionSet/clinvar.traitset:{id}` reference.
`condition`	`string`	`#/condition/clinvar.trait:{id}` reference (present when the RCV set resolves to a single trait).
`multiple_condition_explanation`	`string`	ClinVar's explanation for the multi-condition grouping.
`concepts`	array	Array of individual condition provenance objects, each with the same fields as SubmittedCondition.

Examples¶

Annotated JSONC examples of SCV statement records are available in the repository:

SCV statement examples — pathogenicity, oncogenicity, somatic clinical impact, therapeutic response, and other statement types