ensembl_vep read
scidex.forge.ensembl_vep
Query Ensembl VEP (Variant Effect Predictor) for molecular consequence annotations on a genetic variant (rsID or HGVS). Returns transcript-level consequences sorted by impact severity (HIGH → MODERATE → LOW → MODIFIER), with SIFT/PolyPhen scores and amino acid changes. Third variant annotation layer alongside forge_gnomad_variant (population AF) and forge_clinvar_variant (clinical significance). REST API: https://rest.ensembl.org — free, no auth.
Invoke
Calls scidex.tool.invoke on the substrate with
this tool name. Edit the JSON below — it must match the
input schema. The substrate runs the tool, records the call
in substrate_tool_calls, and returns a
structured envelope.
Sign in to invoke this tool. Schema and curl snippet are visible to anyone.
Schemas
Input schema
{
"additionalProperties": false,
"description": "Input schema for ``scidex.forge.ensembl_vep``.",
"properties": {
"variant_id": {
"description": "Variant identifier: dbSNP rsID (e.g. ``rs699``) or HGVS notation (e.g. ``ENST00000357654.9:c.5340A>G``). rsIDs are the most common input for human disease variants.",
"maxLength": 256,
"minLength": 1,
"title": "Variant Id",
"type": "string"
},
"species": {
"default": "human",
"description": "Species name for VEP lookup. Defaults to ``human``. Other Ensembl species names (e.g. ``mus_musculus``) are also accepted.",
"maxLength": 64,
"title": "Species",
"type": "string"
},
"canonical_only": {
"default": true,
"description": "If True (default), return only the canonical transcript consequence per gene. If False, return all transcript consequences.",
"title": "Canonical Only",
"type": "boolean"
}
},
"required": [
"variant_id"
],
"title": "ForgeEnsemblVEPIn",
"type": "object"
}Output schema
{
"$defs": {
"VEPConsequence": {
"description": "One transcript-level VEP consequence annotation.",
"properties": {
"transcript_id": {
"description": "Ensembl transcript ID (e.g. ENST00000357654).",
"title": "Transcript Id",
"type": "string"
},
"gene_symbol": {
"default": "",
"description": "HGNC gene symbol (e.g. BRCA1).",
"title": "Gene Symbol",
"type": "string"
},
"gene_id": {
"default": "",
"description": "Ensembl gene ID (e.g. ENSG00000012048).",
"title": "Gene Id",
"type": "string"
},
"impact": {
"default": "MODIFIER",
"description": "VEP impact tier: HIGH, MODERATE, LOW, or MODIFIER.",
"title": "Impact",
"type": "string"
},
"consequence_terms": {
"description": "SO consequence terms (e.g. missense_variant, frameshift_variant, splice_donor_variant). Multiple terms may apply to one transcript.",
"items": {
"type": "string"
},
"title": "Consequence Terms",
"type": "array"
},
"amino_acids": {
"default": "",
"description": "Amino acid change in ref/alt notation (e.g. 'S/L' for Ser→Leu). Empty string for non-coding consequences.",
"title": "Amino Acids",
"type": "string"
},
"codons": {
"default": "",
"description": "Codon change in ref/alt notation (e.g. 'tCg/tTg'). Empty for non-coding.",
"title": "Codons",
"type": "string"
},
"sift_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "SIFT score in [0.0, 1.0]. Values < 0.05 predict deleterious effect. None if not predicted (non-missense or missing data).",
"title": "Sift Score"
},
"sift_prediction": {
"default": "",
"description": "SIFT qualitative call: 'deleterious', 'tolerated', or ''.",
"title": "Sift Prediction",
"type": "string"
},
"polyphen_score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "PolyPhen-2 HumVar score in [0.0, 1.0]. Values > 0.908 predict probably_damaging. None if not predicted.",
"title": "Polyphen Score"
},
"polyphen_prediction": {
"default": "",
"description": "PolyPhen-2 qualitative call: 'probably_damaging', 'possibly_damaging', 'benign', or ''.",
"title": "Polyphen Prediction",
"type": "string"
},
"canonical": {
"default": false,
"description": "True if this transcript is the Ensembl canonical transcript for the gene.",
"title": "Canonical",
"type": "boolean"
},
"biotype": {
"default": "",
"description": "Ensembl transcript biotype (e.g. 'protein_coding', 'lncRNA').",
"title": "Biotype",
"type": "string"
}
},
"required": [
"transcript_id"
],
"title": "VEPConsequence",
"type": "object"
}
},
"description": "Response shape for ``scidex.forge.ensembl_vep``.",
"properties": {
"variant_id": {
"description": "The queried variant identifier.",
"title": "Variant Id",
"type": "string"
},
"most_severe_consequence": {
"default": "",
"description": "The most severe consequence term across all transcripts (as reported by Ensembl VEP).",
"title": "Most Severe Consequence",
"type": "string"
},
"consequences": {
"description": "VEP consequence annotations sorted by impact severity (HIGH → MODERATE → LOW → MODIFIER).",
"items": {
"$ref": "#/$defs/VEPConsequence"
},
"title": "Consequences",
"type": "array"
},
"total_transcripts": {
"default": 0,
"description": "Total number of transcript consequences returned (after canonical filter).",
"title": "Total Transcripts",
"type": "integer"
},
"took_ms": {
"description": "Wall-clock time for the upstream call.",
"title": "Took Ms",
"type": "integer"
}
},
"required": [
"variant_id",
"took_ms"
],
"title": "ForgeEnsemblVEPOut",
"type": "object"
}curl snippet
Replace $SCIDEX_JWT with a valid bearer token. Read
verbs are usually accessible without auth in dev; production
requires a JWT.
curl -sS -X POST '/api/scidex/forge/ensembl_vep' \
-H 'authorization: Bearer $SCIDEX_JWT' \
-H 'content-type: application/json' \
-d '{
"variant_id": ""
}'Discussion
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