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:

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.

Quality¶

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

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

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"
  }
]

Citations¶

reportedIn lists the submission's citations, and specifiedBy.reportedIn holds the citation for the assertion method. Each is a VA-Spec Document, one per ClinVar citation. A citation that ClinVar lists with several ids — ACMG 2015 has a PubMed id, a PMC id and a DOI — is a single Document:

{
  "type": "Document",
  "name": "ACMG, 2015",
  "documentType": "general",
  "pmid": "25741868",
  "doi": "10.1038/gim.2015.30",
  "urls": [
    "https://pubmed.ncbi.nlm.nih.gov/25741868",
    "https://europepmc.org/article/PMC/4544753",
    "https://doi.org/10.1038/gim.2015.30"
  ]
}

• name is ClinVar's short label for the citation and documentType is ClinVar's citation type (general, practice guideline, review, Suggested Reading or file in FileTrack), both verbatim and present only when ClinVar gives them. The same holds for the method citation in specifiedBy.reportedIn
• urls holds every resolvable URL, ClinVar's own URL first; a citation ClinVar gives only as a URL — a CIViC evidence link, for example — is {"type": "Document", "urls": ["https://civicdb.org/links/evidence/4846"]}
• A citation that is only free text has no pmid, doi or urls. Its text is kept verbatim in the clinvarCitationText extension. Such text is often not a reference, e.g. a list of ACMG criteria.

The pipeline never changes ClinVar's citation data silently. When an invalid id is repaired, the Document's extensions keep the original:

{
  "type": "Document",
  "documentType": "general",
  "doi": "10.1155/2023/2564200",
  "urls": ["https://doi.org/10.1155/2023/2564200"],
  "extensions": [
    { "name": "originalClinvarCitation", "value": "doi:10.1155/2023/2564200" },
    { "name": "citationRepaired", "value": true }
  ]
}

An id that cannot be used, such as a DOI recorded as https, yields no doi or URL. It appears only as { "name": "invalidClinvarCitation", "value": "https" }. Method.reportedIn holds one Document. When ClinVar lists more than one citation for an assertion method, the first stays there and the rest are Documents in the Method's additionalClinvarMethodCitations extension. The full list of citation extensions and repair rules is on the Final Statements pipeline page.

Proposition¶

SCV propositions are delivered across the four proposition bundle sections (propositionPathogenicity, propositionOncogenicity, propositionSomaticClinicalImpact, propositionClinvarCustom) by meaning, referenced by #/proposition<Meaning>/{id}. The proposition ID combines the SCV accession with an uppercase proposition type code:

SCV001234567-PATH

A resolved proposition contains:

Proposition Types¶

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": "#/propositionSomaticClinicalImpact/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¶

Classification Extensions¶

Extensions on the classification MappableConcept within the Statement.

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.

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.

SubmittedConditionSet¶

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

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