Genebe Tools

Configuration File: genebe_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

GeneBe_classify_variant (Type: GeneBeTool)

Classify a germline variant under the ACMG/AMP guidelines using GeneBe (genebe.net). Given chromo…

GeneBe_classify_variant tool specification

Tool Information:

  • Name: GeneBe_classify_variant

  • Type: GeneBeTool

  • Description: Classify a germline variant under the ACMG/AMP guidelines using GeneBe (genebe.net). Given chromosome, position, ref and alt alleles on genome build hg38 (default) or hg19, returns the ACMG verdict (e.g. Pathogenic), the numeric ACMG score, and the exact triggered criteria (e.g. PS3,PM1,PM2,PM5,PP2,PP3_Moderate,PP5), plus gene symbol, transcript, HGVS c./p., predicted effect, dbSNP id, gnomAD allele frequency, ClinVar classification, and an AlphaMissense score. This is an independent second opinion complementary to InterVar_classify_variant (a different group’s ACMG implementation) — cross-check both for borderline variants. Public API, no key required (a free account raises the rate limit).

Parameters:

  • chr (string) (required) Chromosome, e.g. ‘7’, ‘X’ (a ‘chr’ prefix is also accepted).

  • pos (integer) (required) 1-based genomic position of the variant, e.g. 140753336.

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

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

  • genome (string) (optional) Genome build: ‘hg38’ (default) / ‘GRCh38’ or ‘hg19’ / ‘GRCh37’.

Example Usage:

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

GeneBe_classify_variants_batch (Type: GeneBeTool)

Batch-classify up to 1000 germline variants under the ACMG/AMP guidelines in a single GeneBe (gen…

GeneBe_classify_variants_batch tool specification

Tool Information:

  • Name: GeneBe_classify_variants_batch

  • Type: GeneBeTool

  • Description: Batch-classify up to 1000 germline variants under the ACMG/AMP guidelines in a single GeneBe (genebe.net) request. Provide ‘variants’ as a JSON array of objects, each with chr, pos, ref, alt on genome build hg38 (default) or hg19. For every variant GeneBe returns the full ACMG output: the verdict (e.g. Pathogenic), the numeric ACMG score, the exact triggered criteria (e.g. PS3,PM1,PM2,PM5,PP2,PP3_Moderate,PP5), per-gene HGVS c./p. (acmg_by_gene), AlphaMissense score/prediction, gnomAD allele frequency, and ClinVar classification. Use this instead of calling GeneBe_classify_variant once per variant when you have many variants. Public API, no key required (a free account raises the rate limit). Example: [{“chr”:”7”,”pos”:140753336,”ref”:”A”,”alt”:”T”},{“chr”:”22”,”pos”:28695868,”ref”:”AG”,”alt”:”A”}] returns BRAF p.Val600Glu Pathogenic score 14 plus the second variant.

Parameters:

  • variants (array) (required) List of variants to classify (max 1000). Each item is an object with chr, pos, ref, alt.

  • genome (string) (optional) Genome build for ALL variants in the batch: ‘hg38’ (default) / ‘GRCh38’ or ‘hg19’ / ‘GRCh37’.

Example Usage:

query = {
    "name": "GeneBe_classify_variants_batch",
    "arguments": {
        "variants": ["item1", "item2"]
    }
}
result = tu.run(query)