Cortexa research tool·genomics·opencravat

OpenCRAVAT Annotate Variant

Annotate a single genomic variant using OpenCRAVAT with 182+ annotation sources including ClinVar, gnomAD, SIFT, PolyPhen-2, REVEL, AlphaMissense, SpliceAI, GERP, PhastCons, DANN, FATHMM, and more. Returns gene name, amino acid change, consequence type, and all requested annotator results. Input: chromosome, position (1-based, GRCh38), reference and alternate alleles. Optionally specify which annotators to use (comma-separated).

Livelast probed 2026-04-30 23:07Z· 93msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 93ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "alt": {
      "description": "Alias for alt_base. Alternate allele.",
      "type": [
        "string",
        "null"
      ]
    },
    "alt_base": {
      "description": "Alternate allele (e.g., 'T', 'A', 'G', 'C')",
      "type": [
        "string",
        "null"
      ]
    },
    "annotators": {
      "description": "Comma-separated annotator names (e.g., 'clinvar,gnomad3,sift,polyphen2,revel,alphamissense'). If omitted, returns only basic variant annotation (gene, consequence). Common annotators: clinvar, gnomad3, sift, polyphen2, cadd_exome, revel, alphamissense, spliceai, dann, fathmm, gerp, phastcons, dbsnp, mutation_assessor, provean, vest, primateai, lrt.",
      "type": [
        "string",
        "null"
      ]
    },
    "chrom": {
      "description": "Chromosome (e.g., 'chr17', 'chr7', '17'). 'chr' prefix added automatically if missing.",
      "type": [
        "string",
        "null"
      ]
    },
    "chromosome": {
      "description": "Alias for chrom. Chromosome (e.g., 'chr17', 'chr7', '17').",
      "type": [
        "string",
        "null"
      ]
    },
    "pos": {
      "description": "Genomic position (1-based, GRCh38 coordinates)",
      "type": [
        "integer",
        "null"
      ]
    },
    "position": {
      "description": "Alias for pos. Genomic position (1-based, GRCh38 coordinates).",
      "type": [
        "integer",
        "null"
      ]
    },
    "ref": {
      "description": "Alias for ref_base. Reference allele.",
      "type": [
        "string",
        "null"
      ]
    },
    "ref_base": {
      "description": "Reference allele (e.g., 'C', 'A', 'G', 'T')",
      "type": [
        "string",
        "null"
      ]
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

Default OpenCRAVAT Annotate Variant call

public-safeinput

{}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_OpenCRAVAT_annotate_variant
Tool name: OpenCRAVAT_annotate_variant
Added: 2026-04-30 22:47Z
Tags: tooluniverse

OpenCRAVAT Annotate Variant

Livelast probed 2026-04-30 23:07Z· 93msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "alt": { "description": "Alias for alt_base. Alternate allele.", "type": [ "string", "null" ] }, "alt_base": { "description": "Alternate allele (e.g., 'T', 'A', 'G', 'C')", "type": [ "string", "null" ] }, "annotators": { "description": "Comma-separated annotator names (e.g., 'clinvar,gnomad3,sift,polyphen2,revel,alphamissense'). If omitted, returns only basic variant annotation (gene, consequence). Common annotators: clinvar, gnomad3, sift, polyphen2, cadd_exome, revel, alphamissense, spliceai, dann, fathmm, gerp, phastcons, dbsnp, mutation_assessor, provean, vest, primateai, lrt.", "type": [ "string", "null" ] }, "chrom": { "description": "Chromosome (e.g., 'chr17', 'chr7', '17'). 'chr' prefix added automatically if missing.", "type": [ "string", "null" ] }, "chromosome": { "description": "Alias for chrom. Chromosome (e.g., 'chr17', 'chr7', '17').", "type": [ "string", "null" ] }, "pos": { "description": "Genomic position (1-based, GRCh38 coordinates)", "type": [ "integer", "null" ] }, "position": { "description": "Alias for pos. Genomic position (1-based, GRCh38 coordinates).", "type": [ "integer", "null" ] }, "ref": { "description": "Alias for ref_base. Reference allele.", "type": [ "string", "null" ] }, "ref_base": { "description": "Reference allele (e.g., 'C', 'A', 'G', 'T')", "type": [ "string", "null" ] } }, "required": [], "type": "object" }