gnomAD MCP Server

@koido

About gnomAD MCP Server

This MCP server provides a programmatic interface to the Genome Aggregation Database (gnomAD) API, supporting multiple API versions (v2.1.1, v3.1.2, v4.1.0).

#bioinformatics #gnomad #mcp-server

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "gnomad": {
      "command": "uv",
      "args": [
        "--directory",
        "where you cloned the repo",
        "run",
        "server.py"
      ],
      "env": {}
    }
  }
}

Tools

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Overview

What is gnomAD MCP Server?

The gnomAD MCP Server provides a programmatic interface to the Genome Aggregation Database (gnomAD) API, supporting multiple API versions (v2.1.1, v3.1.2, v4.1.0). It abstracts version-specific field and schema differences, exposing a unified API for downstream tools and users.

How to use gnomAD MCP Server?

Install dependencies with uv sync, activate the virtual environment with . .venv/bin/activate, test the server with uv --directory ./ run mcp dev server.py, and add it to your MCP client configuration (Claude, Cursor, etc.) using the JSON format shown in the README.

Key features of gnomAD MCP Server

Supports three gnomAD API versions (v2, v3, v4)
Queries include variant, gene, region, ClinVar, STR, and more
Uses QueryTemplateEngine for version-specific GraphQL queries
Unified API abstracts version-specific field differences
Python >= 3.13 required; uses FastMCP, aiohttp, httpx

Use cases of gnomAD MCP Server

Retrieve variant metadata and population frequency data by variantId
Search for genes by symbol or name across gnomAD versions
Retrieve ClinVar variant data and clinical significance
Obtain gene metadata and constraint metrics (v4 only)
Retrieve structural variant, copy number variant, and repeat data

FAQ from gnomAD MCP Server

What gnomAD API versions are supported?

v2.1.1 (gnomad_r2), v3.1.2 (gnomad_r3), and v4.1.0 (gnomad_r4) are supported, with varying query availability per version.

What queries are available for gnomAD MCP Server?

Queries include get_variant_info, get_clinvar_variant_info, search_for_variants, search_for_genes, and more; v4 supports additional queries like get_gene_info, get_region_info, and get_str_info.

What are the runtime requirements?

Python >= 3.13 with dependencies aiohttp >= 3.11.18, fastmcp >= 2.2.1, gql >= 3.5.2, httpx >= 0.28.1, mcp[cli] >= 1.6.0, nest-asyncio >= 1.6.0, and testing packages.

How is gnomAD MCP Server configured for use with clients?

Add to MCP client config (Claude, Cursor, etc.) with command "uv", args ["--directory", "repo_path", "run", "server.py"], and an empty env object.

What is the current status of gnomAD MCP Server?

Under active development; APIs and features may change without notice.

Frequently asked questions