VEP: Variant Effect
vep_annotateAnnotate a plant variant from an Ensembl region and alternate allele; returns primary molecular consequence, IMPACT, and SIFT scores per overlapping transcript.
Instructions
Predict a variant's molecular consequences with Ensembl VEP (rest.ensembl.org; free, no key). Variant-first (not locus-first): supply an Ensembl region (chr:start-end:strand, e.g. '1:10000-10000:1') and an alternate allele (e.g. 'C'); returns the most-severe consequence plus one row per overlapping transcript (consequence terms, IMPACT, and SIFT when the variant is coding-missense; the polyphen fields stay null, as Ensembl runs PolyPhen for human only). found=false when Ensembl reports no overlapping feature. Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| allele | Yes | Alternate allele, e.g. 'C' (or 'A/C', an insertion, etc.) | |
| region | Yes | Ensembl region chr:start-end:strand, e.g. '1:10000-10000:1' | |
| organism | No | Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid | arabidopsis_thaliana |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| end | No | ||
| found | Yes | True if VEP returned an overlapping feature | |
| input | No | VEP echo of the parsed input | |
| start | No | ||
| allele | Yes | Alternate allele, e.g. 'C' | |
| region | Yes | Ensembl region, e.g. '1:10000-10000:1' | |
| organism | Yes | Resolved Ensembl species slug | |
| allele_string | No | ||
| assembly_name | No | Assembly the call is against | |
| seq_region_name | No | ||
| most_severe_consequence | No | Most severe SO term | |
| transcript_consequences | No | Per-transcript {gene_id, transcript_id, consequence_terms, impact, sift_*, …} |