ClinvarCategoricalVariant¶
Trial Use
May change in future releases. See the GKM Maturity Model.
The Clinvar specific representations of categorical variants.
JSON Schema: ClinvarCategoricalVariant
One of:
- ClinvarCanonicalAllele
- ClinvarCategoricalCnvChange
- ClinvarCategoricalCnvCount
- ClinvarNonConstrainedVariant
Extensions¶
These extensions are defined for ClinvarCategoricalVariant.
ExtensionAssembly¶
An extension item for the assembly associated with a Clinvar variant.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'assembly'. |
value |
string |
0..1 | The assembly of the variant as provided by Clinvar. It must be one of the following: 'GRCh37', 'GRCh38', or 'NCBI36'. |
ExtensionCategoricalVariationType¶
The Cat-VRS category assigned to this variation: CanonicalAllele, CategoricalCnvChange, CategoricalCnvCount, or Undefined. Determines which constraint types are generated.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'categoricalVariationType'. |
value |
string |
0..1 | The type of categorical variant. It must be one of the following: CanonicalAllele, CategoricalCnvChange, CategoricalCnvCount, or Undefined. |
ExtensionClinvarCytogeneticLocation¶
The cytogenetic band location of the variation (e.g., 1p36.22, 17q21.31). Present when ClinVar provides a cytogenetic location.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'clinvarCytogeneticLocation'. |
value |
string |
0..1 | The cytogenetic location of the variant as provided by Clinvar. |
ExtensionClinvarGeneList¶
Gene associations for this variation from ClinVar, including Entrez gene IDs, HGNC IDs, gene symbols, relationship types, and identifier IRIs.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'clinvarGeneList'. |
value |
GeneListItem[] (unordered) | 0..m | Clinvar's data structure for representing genes associated with a clinvar variant. |
ExtensionClinvarHgvsList¶
Complete list of HGVS expressions from ClinVar for a variant, including nucleotide and protein expressions, molecular consequences (SO terms), and MANE transcript designations.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'clinvarHgvsList'. |
value |
HgvsListItem[] (unordered) | 0..m | Clinvar's data structure for representing the HGVS expressions, mane select/plus settings and molecular consequence for dervied genomic/transcript sequence alignmnents and protein sequence projections originating from the definining allele or location for CNVs. |
ExtensionClinvarSubclassType¶
The variation subclass as reported by ClinVar (e.g., SimpleAllele, Haplotype, CompoundHeterozygote). Present when ClinVar provides a subclass type.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'clinvarSubclassType'. |
value |
string |
0..1 | The subclass type of the variant as provided by Clinvar. It must be one of the following: 'Genotype', 'Haplotype', or 'SimpleAllele'. |
ExtensionClinvarVariationType¶
The variation type as reported by ClinVar (e.g., Deletion, single nucleotide variant, Duplication, Indel). Present when ClinVar provides a variation type.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'clinvarVariationType'. |
value |
string |
0..1 | The type of variant as provided by Clinvar. It must be one of the following: 'Complex', 'CompoundHeterozygote', 'copy number gain', 'copy number loss', 'Deletion', 'Diplotype', 'Distinct chromosomes', 'Duplication', 'fusion', 'Haplotype, single variant', 'Haplotype', 'Indel', 'Insertion', 'Inversion', 'Microsatellite', 'Phase unknown', 'protein only', 'single nucleotide variant', 'Tandem duplication', 'Translocation', or 'Variation'. |
ExtensionDefiningVrsVariationType¶
The VRS class assigned during variation identity processing (e.g., Allele, CopyNumberChange, CopyNumberCount, Not Available). Reflects the upstream classification used to route the variant through VRS processing.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'definingVrsVariationType'. |
value |
string |
0..1 | The type of categorical variant. It must be one of the following: Allele, CopyNumberChange, CopyNumberCount, Haplotype, Unknown, or Not Available. |
ExtensionVrsPreProcessingIssue¶
Issues detected during VRS pre-processing of the variation's input expressions. Present only when issues exist. May contain multiple issues separated by newlines
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'vrsPreProcessingIssue'. |
value |
string |
0..1 | The VRS processing errors associated with the Clinvar variant. |
ExtensionsVrsProcessingException¶
Errors returned by the external VRS Python processing service. Present only when errors occurred during VRS resolution.
| Field | Type | Limits | Description |
|---|---|---|---|
name |
string |
0..1 | Must be 'vrsProcessingException'. |
value |
string |
0..1 | The VRS processing errors associated with the Clinvar variant. |