MCP server

Gnomad

io.github.pipeworx-io/gnomad

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

gnomAD MCP — Broad Institute Genome Aggregation Database (GraphQL).

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

47

Token cost

About 27,581 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http gnomad https://gateway.pipeworx.io/gnomad/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.gnomad]
url = "https://gateway.pipeworx.io/gnomad/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"gnomad":{"type":"http","url":"https://gateway.pipeworx.io/gnomad/mcp"}}}

Antigravity

agy mcp add gnomad https://gateway.pipeworx.io/gnomad/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"gnomad","server_url":"https://gateway.pipeworx.io/gnomad/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"gnomad","server_url":"https://gateway.pipeworx.io/gnomad/mcp"}

Tools

• gene ~242 tokens
  Gene info + its variants. Accepts gene symbol (e.g. "BRCA1") or Ensembl gene id. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.
• region ~464 tokens
  Variants in a genomic region (≤25kb recommended). You MUST say which genome build your start/stop are in via assembly — there is no default, because a position is valid in both builds and a wrong guess returns real variants from the wrong locus rather than an error. Variants are paged (default 500,
• search ~126 tokens
  Autocomplete-style search across gnomAD genes and variants by free-text query; returns matching Ensembl gene IDs with symbols, and matching variant IDs (an rsid resolves here). Use to resolve a partial gene name, symbol or rsid before calling gene or variant.
• transcript ~288 tokens
  Fetch gnomAD variant data for an Ensembl transcript (ENST…), returning transcript coordinates, gene symbol, chromosome position, and per-variant allele counts (ac/an) from exome and genome datasets. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_of
• variant ~158 tokens
  Variant by chr-pos-ref-alt (e.g. "1-55051215-G-A") or rsid (e.g. "rs1801133"). Coordinates must match the dataset's genome build: the default gnomad_r4 is GRCh38, so a GRCh37/hg19 position will not be found — pass dataset "gnomad_r2_1" for GRCh37.

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