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Condition Extensions

Overview

Condition and condition set records contain extensions arrays at two structural levels — on each individual Condition and on the outer Condition or ConditionSet wrapper. Extensions carry ClinVar-specific metadata, submitter-provided cross-references, and trait assignment provenance that are not part of the GA4GH VA-Spec condition model but are essential for tracing how each SCV's submitted traits were resolved.

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

Note

The aliases field (alternate names/synonyms for a condition) is a top-level field on the condition record, not an extension. It is an array of strings, present only when the trait has synonyms.

Extension Reference

Extension (section, type) Description
clinvarTraitId
Condition
string		 The ClinVar trait ID for this condition. Corresponds to the id attribute on the Trait element in ClinVar XML. 
{ "name": "clinvarTraitId", "value": "9580" }
clinvarTraitType
Condition
string		 The trait type as classified by ClinVar (e.g., Disease, Finding, PhenotypeInstruction, NamedProteinVariant). 
{ "name": "clinvarTraitType", "value": "Disease" }
submittedScvXrefs
Condition
array<SubmittedXref>		 The original cross-references submitted by the submitter for this trait, preserved as-is. Present only when the submitter provided xrefs. See Submitted SCV Xrefs custom extension structure below. 
{ "name": "submittedScvXrefs", "value": [...] }
submittedScvTraitAssignment
Condition
string		 Describes how the SCV trait was matched to a ClinVar trait mapping record during condition mapping (e.g., scv trait: preferred name 'breast cancer'). Present only when a trait mapping match was found. 
{ "name": "submittedScvTraitAssignment", "value": "scv trait: preferred name 'breast-ovarian cancer, familial, 1'" }
clinvarScvTraitAssignment
Condition
string		 The assignment stage that resolved this SCV trait to a normalized RCV trait. See the Assignment Type Reference in the condition mapping documentation for all possible values. 
{ "name": "clinvarScvTraitAssignment", "value": "rcv-tm medgen id" }
clinvarScvTraitMappingType:ref(val)
Condition
string		 The ClinVar trait mapping details formatted as type:ref(val). Shows the mapping type, reference field, and matched value from the trait mapping record. Present only when a trait mapping was used. 
{ "name": "clinvarScvTraitMappingType:ref(val)", "value": "name:preferred(breast-ovarian cancer, familial, 1)" }
clinvarTraitSetType
Condition / ConditionSet
string		 The RCV-level trait set type as assigned by ClinVar (e.g., Disease, Finding, DrugResponse, TraitChoice). Present on the outer wrapper of both single-condition and multi-condition records. 
{ "name": "clinvarTraitSetType", "value": "Disease" }
clinvarTraitSetId
Condition / ConditionSet
string		 The ClinVar trait set ID. Corresponds to the id attribute on the RCV's TraitSet element. 
{ "name": "clinvarTraitSetId", "value": "2" }
submittedScvTraitSetType
Condition / ConditionSet
string		 The submitter's original trait set type, included only when it differs from the RCV-assigned trait set type. Useful for identifying cases where ClinVar re-classified the trait set type. 
{ "name": "submittedScvTraitSetType", "value": "Finding" }

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 SCV Xrefs

The submittedScvXrefs extension contains an array of cross-reference objects as originally submitted by the submitter. These are preserved without normalization to maintain a record of what the submitter provided.

Field (type) Description
code
string		 The cross-reference identifier as submitted (e.g., C0677776, 604370, MONDO:0011450).
system
string		 The database name as submitted. Common values include MedGen, OMIM, MONDO, HP, HPO, MeSH, MESH, Orphanet, UMLS, GeneReviews, and OMIM phenotypic series.

Example

[
  { "code": "C0677776", "system": "MedGen" },
  { "code": "604370", "system": "OMIM" }
]