Intervar Tools

Configuration File: intervar_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the intervar_tools.json configuration file.

Available Tools

InterVar_classify_variant (Type: InterVarTool)

Classify a germline variant using ACMG/AMP 2015 standards (InterVar). Returns the clinical signif…

InterVar_classify_variant tool specification

Tool Information:

  • Name: InterVar_classify_variant

  • Type: InterVarTool

  • Description: Classify a germline variant using ACMG/AMP 2015 standards (InterVar). Returns the clinical significance category — Pathogenic, Likely Pathogenic, Uncertain Significance, Likely Benign, or Benign — plus the activation status of all 28 evidence criteria (PVS1, PS1-PS4, PM1-PM6, PP1-PP5, BA1, BP1-BP7, BS1-BS4). Input requires genomic coordinates in hg19 or hg38. No API key needed. Example: BRCA1 c.5266dupC (chr17:41245466 G>A in hg19) is Likely Pathogenic with PM2+PP3+PP5.

Parameters:

  • chrom (string) (required) Chromosome number or name. Can include ‘chr’ prefix (e.g., ‘17’, ‘chr17’, ‘X’).

  • pos (integer) (required) Genomic position (1-based).

  • ref (string) (required) Reference allele (e.g., ‘G’, ‘A’, ‘ATCG’).

  • alt (string) (required) Alternate allele (e.g., ‘A’, ‘T’, ‘C’).

  • build (string) (optional) Genome build. Default: hg19.

Example Usage:

query = {
    "name": "InterVar_classify_variant",
    "arguments": {
        "chrom": "example_value",
        "pos": 10,
        "ref": "example_value",
        "alt": "example_value"
    }
}
result = tu.run(query)