Variant Effect Prediction from HGVS Notation: Consequence, SIFT, PolyPhen (Ensembl VEP)
ensembl/variant-effect
Predicts the consequences of one genetic variant written in HGVS notation (genomic, coding or protein, for example ENST00000366667:c.803C>T) using the Ensembl Variant Effect Predictor: most severe consequence, and for each affected transcript the gene, impact, amino-acid change, codons and SIFT and PolyPhen predictions, plus known co-located variants. Default annotation only; no third-party plugin scores. A notation that cannot be parsed returns a validation error. Ensembl data, passed through unmodified and served by Eden Engine; not an official Ensembl product.
Price
$0.0026 per call
You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.
Data source
Source: Ensembl (EMBL-EBI), https://www.ensembl.org, retrieved through the Ensembl REST API. Served by Eden Engine; not an official Ensembl product.
Use it
Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.
Connect once and your AI can find and run this tool, and any other it needs.
// 1. search: find the tool
omnial_search({ query: "what you need" })
// 2. inspect: price and input schema
omnial_inspect({ tool: "ensembl/variant-effect" })
// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "ensembl/variant-effect" })
// 4. run: price the exact call first, then run it
omnial_execute({ tool: "ensembl/variant-effect", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "ensembl/variant-effect", input: { /* ... */ } })
// 5. settle: the call is charged when it finishes, nothing to doNot connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.
Pricing
Every charge this tool can incur.
| Charge | Price |
|---|---|
Per call | $0.0026 |
- Updated
- Oct 20, 2026
Input and output schemas
Input schema
{
"type": "object",
"required": [
"hgvs_notation"
],
"properties": {
"species": {
"type": "string",
"default": "human",
"pattern": "^[a-z][a-z0-9_]{1,59}$",
"description": "Ensembl species name or alias, lowercase, for example human or homo_sapiens. Defaults to human."
},
"hgvs_notation": {
"type": "string",
"pattern": "^[A-Za-z0-9_.:>()=*+-]{3,200}$",
"description": "One variant in HGVS notation: genomic (g.), coding (c.) or protein (p.), against a chromosome, gene, transcript or protein id. Examples: ENST00000366667:c.803C>T, 9:g.22125504G>C, ENST00000003084:c.1431_1433delTTC."
}
},
"additionalProperties": false
}Output schema
{
"type": "object",
"required": [
"results"
],
"properties": {
"results": {
"type": "array",
"items": {
"type": "object",
"properties": {
"id": {
"type": "string",
"description": "The submitted notation."
},
"end": {
"type": "integer"
},
"input": {
"type": "string",
"description": "The submitted notation, echoed."
},
"start": {
"type": "integer"
},
"strand": {
"type": "integer"
},
"allele_string": {
"type": "string",
"description": "Reference and alternate allele, e.g. C/T."
},
"assembly_name": {
"type": "string"
},
"seq_region_name": {
"type": "string"
},
"colocated_variants": {
"type": "array",
"items": {
"type": "object",
"additionalProperties": true
},
"description": "Known variants at the same position, with ids and population frequencies."
},
"most_severe_consequence": {
"type": "string",
"description": "The most severe Sequence Ontology term, for example missense_variant."
},
"transcript_consequences": {
"type": "array",
"items": {
"type": "object",
"additionalProperties": true
},
"description": "One entry per affected transcript: gene_id, gene_symbol, transcript_id, consequence_terms, impact, amino_acids, codons, sift_prediction and sift_score, polyphen_prediction and polyphen_score where the service computes them."
}
},
"additionalProperties": true
}
}
},
"description": "One VEP result per variant submitted (always one here)."
}