ClinvarGeneContextQualifier¶
Trial Use
May change in future releases. See the GKM Maturity Model.
The gene context qualifier on a ClinVar SCV proposition: a gene MappableConcept. When it carries a 'geneContextSource' extension, that extension's value MUST be one of the four values defined by ExtensionGeneContextSource. Other extensions (e.g. 'submittedGeneSymbols') are not constrained here.
JSON Schema: ClinvarGeneContextQualifier
Some ClinvarGeneContextQualifier attributes are inherited from MappableConcept.
Information Model¶
| Field | Type | Limits | Description |
|---|---|---|---|
id |
string |
0..1 | The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another. |
type |
string |
0..1 | MUST be "MappableConcept". |
name |
string |
0..1 | A primary name for the concept. |
description |
string |
0..1 | A free-text description of the Entity. |
aliases |
string[] (unordered) |
0..m | Alternative name(s) for the Entity. |
extensions |
Extension[] (unordered) | 0..m | Extensions on the qualifier. An item named 'geneContextSource' must match ExtensionGeneContextSource. |
conceptType |
string |
0..1 | A term indicating the type of concept being represented by the MappableConcept. |
primaryCoding |
Coding | 0..1 | A primary coding for the concept. |
mappings |
ConceptMapping[] (unordered) | 0..m | A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. |
Extensions¶
These extensions are defined for ClinvarGeneContextQualifier.
ExtensionGeneContextSource¶
Where the gene on a SCV proposition's geneContextQualifier came from, compared with the gene symbols the submitter gave.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'geneContextSource'. |
value |
string |
0..1 | submittedSymbolMatches: the submitter's symbols include the qualifier's symbol. submittedSymbolDiffers: the submitter gave symbols, but none equals the qualifier's symbol (most are previous symbols of the same gene). inferredFromVariant: the submitter gave no symbols. submittedNotNormalized: the variant has no single representative gene, so the qualifier is a placeholder named with the submitter's symbol(s). Symbols are compared trimmed and case-insensitively. |