vep_region_single
Annotate a genetic variant by providing genomic region and allele, retrieving effect predictions including pathogenicity scores, conservation, and regulatory features.
Instructions
Annotate a variant using genomic region and allele
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| species | Yes | Species name (e.g., 'homo_sapiens', 'mus_musculus') | homo_sapiens |
| region | Yes | Genomic region (pos or range, optionally with allele) | |
| allele | Yes | Allele base (A,C,G,T) | |
| 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) |