SCV Statement Extensions

Overview

Schema Reference

For the canonical extension reference tables (extension names, value types, and descriptions), see SCV Statements — Extensions.

SCV statement records contain extensions arrays at three structural levels — on the top-level Statement, on the classification object, and on proposition qualifier objects (geneContextQualifier, modeOfInheritanceQualifier, penetranceQualifier). Extensions carry ClinVar-specific metadata, submitter-provided values, and formatted descriptions that are not part of the GA4GH VA-Spec statement model but are essential for tracing how each SCV was processed.

All extensions follow the structure { "name": "<extension_name>", "value": <value> }, where the value type varies by extension. Most extensions carry simple string values. Extensions with complex value types — structured condition provenance objects — are documented as custom extension structures in a dedicated section below.

---

Statement Extensions

Extensions on the top-level Statement record.

Extension	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. See Submitted Condition below.
submittedConditionSet	SubmittedConditionSet	Submitted condition set provenance with multiple condition concepts. Present when the SCV maps to multiple conditions. See Submitted Condition Set below.
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.

Example

A typical germline SCV statement extensions array:

[
  { "name": "clinvarScvId", "value": "SCV002769510" },
  { "name": "clinvarScvVersion", "value": "1" },
  {
    "name": "submittedCondition",
    "value": {
      "condition": "#/condition/clinvar.trait:9582",
      "id": "SCV002769510.0",
      "name": "Hemochromatosis",
      "type": "Disease",
      "medgen_id": "C3469186",
      "normalized_match": "#/condition/clinvar.trait:9582",
      "normalized_resolution": "tm reftype xref omim",
      "xrefs": [{ "code": "235200", "system": "OMIM" }],
      "mapping": { "type": "XRef", "ref": "omim", "value": "235200" }
    }
  },
  { "name": "clinvarScvReviewStatus", "value": "criteria provided, single submitter" },
  { "name": "submittedScvLocalKey", "value": "vcgs/unit_1/hg38_NM_000410_3_HFE_c_187C_G" },
  { "name": "submissionLevel", "value": "CP" }
]

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 object within the Statement.

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

Example

{
  "name": "description",
  "value": "for Hemochromatosis\nClassification is based on the criteria provided submission\nMay 2021 by Victorian Clinical Genetics Services, Murdoch Childrens Research Institute"
}

The description template is: for <condition_name>\nClassification is based on the <submission_level_label> submission\n<evaluated_date> by <submitter_name>. When the condition is a multi-condition set, <condition_name> is replaced with <N> conditions. The date is formatted as Mon YYYY or (-) when not available.

---

Qualifier Extensions

Extensions on proposition qualifier objects, preserving the original submitter-provided values.

Extension	Type	Description
submittedGeneSymbols	array<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.

Example

Gene context qualifier with submitted gene symbols:

{
  "conceptType": "gene",
  "name": "KRAS",
  "primaryCoding": { "code": "3845", "name": "KRAS", "system": "https://www.ncbi.nlm.nih.gov/gene/" },
  "extensions": [
    { "name": "submittedGeneSymbols", "value": ["KRAS"] }
  ]
}

---

Custom Extension Structures

Extensions with complex value types use structured objects rather than simple scalars. The structures below define the shape of each custom extension's value field.

Submitted Condition

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

Submitted Condition Set

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 Submitted Condition