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gnomAD MCP Server

@koido

Repository

Basic information

Category

Other

Transports

stdio

Author

koido

Submitted by

Masaru 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

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": {}
    }
  }
}

gnomAD MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

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

Frequently asked questions

1

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.

2

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.

3

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.

4

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.

5

What is the current status of gnomAD MCP Server?

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

Comments

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