GeneBe

Connect Remote server

claude mcp add --transport http genebe-mcp https://mcp.genebe.net/v1/mcp

{
  "mcpServers": {
    "genebe-mcp": {
      "url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}

{
  "servers": {
    "genebe-mcp": {
      "type": "http",
      "url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}

Settings > Connectors > Add custom connector
URL: https://mcp.genebe.net/v1/mcp

Tools 6 found in our last check

• annotate_variant

  Annotate and classify one human genetic variant using GeneBe. Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it). Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores (REVEL, AlphaMiss…

• explain_acmg_decision_path

  Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the…

• convert_variant

  Convert a variant written in any notation into normalized hg38 genomic coordinates. Use when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID), without annotation. Does not classify the variant; use annotate_variant for that.

• get_variant_effects

  List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.

• get_gene

  Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity. Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total_transcripts.

• liftover_coordinate

  Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t). Check `status`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target r…

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