@pipeworx/gnomad

gnomAD MCP — Genome Aggregation Database (Broad Institute) public GraphQL endpoint. Population allele frequencies + variant pathogenicity annotations. Keyless.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

• variant(variant_id, dataset?) — by chr-pos-ref-alt (e.g. 1-55051215-G-A) or rsid
• gene(gene_symbol_or_id, dataset?) — variants in / near a gene
• region(chrom, start, stop, dataset?) — variants in a genomic region
• transcript(transcript_id, dataset?) — variants in / near a transcript
• search(query) — gene / variant search (autocomplete)

dataset defaults to gnomad_r4 (most recent release). Other valid: gnomad_r3, gnomad_r2_1, gnomad_sv_r4, etc.

Data source

https://gnomad.broadinstitute.org/api

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "gnomad": {
      "url": "https://gateway.pipeworx.io/gnomad/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Gnomad data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT