vep_hgvs_single
Annotate a single variant using HGVS notation to retrieve functional effects, pathogenicity scores, and protein domain information.
Instructions
Annotate a single variant using HGVS notation (genomic g., coding c., protein p.)
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| species | Yes | Species name (e.g., 'homo_sapiens', 'mus_musculus') | homo_sapiens |
| hgvs_notation | Yes | HGVS notation (e.g., 'ENST00000366667:c.803C>T', '17:g.41276107A>C', 'ENSP00000401091.1:p.Tyr124Cys') | |
| canonical | No | Include only canonical transcripts per gene | |
| hgvs | No | Include HGVS nomenclature | |
| domains | No | Include protein domain information | |
| ccds | No | Include CCDS transcript identifiers | |
| protein | No | Include protein sequence identifiers | |
| AlphaMissense | No | Include AlphaMissense pathogenicity scores | |
| CADD | No | Include CADD deleteriousness scores | |
| REVEL | No | Include REVEL pathogenicity scores | |
| ClinPred | No | Include ClinPred pathogenicity predictions | |
| Conservation | No | Include conservation scores | |
| Blosum62 | No | Include BLOSUM62 substitution scores | |
| GO | No | Include Gene Ontology annotations | |
| Phenotypes | No | Include phenotype data | |
| tsl | No | Include transcript support level | |
| appris | No | Include APPRIS annotations | |
| mane | No | Include MANE transcript annotations | |
| distance | No | Distance for regulatory features (bp, 0-5000000) | |
| SpliceAI | No | SpliceAI score threshold (0-1) |