GenomeNexus Annotate Mutation

Overview

Annotate a cancer mutation using Genome Nexus (MSK) by specifying chromosome, start, end, reference allele, and variant allele separately. This is an alternative to the HGVS-based annotation for when you have genomic coordinates directly (GRCh37/hg19). Returns the same comprehensive annotation as GenomeNexus_annotate_variant including VEP consequences, SIFT, PolyPhen, AlphaMissense scores, cancer hotspots, and mutation assessor. Example: chr=7, start=140453136, end=140453136, ref=A, alt=T for BRAF V600E.

Status

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

Last probed

1d ago

Last success

1d ago

Last latency

109ms

Schema

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

{
  "properties": {
    "chromosome": {
      "description": "Chromosome (without 'chr' prefix). Examples: '7', '17', '12', 'X'.",
      "type": "string"
    },
    "end": {
      "description": "End position (GRCh37/hg19, 1-based). Same as start for SNVs.",
      "type": "integer"
    },
    "reference_allele": {
      "description": "Reference allele. Example: 'A'.",
      "type": "string"
    },
    "start": {
      "description": "Start position (GRCh37/hg19, 1-based).",
      "type": "integer"
    },
    "variant_allele": {
      "description": "Variant (alternate) allele. Example: 'T'.",
      "type": "string"
    }
  },
  "required": [
    "chromosome",
    "start",
    "end",
    "reference_allele",
    "variant_allele"
  ],
  "type": "object"
}

Examples (1)

{
  "chromosome": "",
  "end": 1,
  "reference_allele": "",
  "start": 1,
  "variant_allele": ""
}

Identifiers

Catalog ID

tu_GenomeNexus_annotate_mutation

Tool name

GenomeNexus_annotate_mutation

Added

2026-04-30 22:47Z

Tags

tooluniverse