gnomAD MCP Server

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.