gnomAD MCP Server

gnomAD MCP Server

Overview

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).
It abstracts version-specific field and schema differences, exposing a unified API for downstream tools and users.

Status

🚧 Under Active Development 🚧

This project is under active development. APIs and features may change without notice.

Supported gnomAD API Versions

• v4.1.0 (gnomad_r4)
• v3.1.2 (gnomad_r3)
• v2.1.1 (gnomad_r2_1)

Supported Queries by Version

The following table summarizes which queries are available for each gnomAD API version:

Query Type	Description	v2	v3	v4
get_gene_info	Retrieve gene metadata and constraint metrics (direct lookup by gene_id/gene_symbol)	❌	❌	✅
get_region_info	Retrieve variant and summary information for a genomic region	❌	❌	✅
get_variant_info	Retrieve variant metadata and population frequency data (by variantId)	✅	✅	✅
get_clinvar_variant_info	Retrieve ClinVar variant data and clinical significance	✅	✅	✅
get_mitochondrial_variant_info	Retrieve mitochondrial variant data and population frequencies	❌	❌	✅
get_structural_variant_info	Retrieve structural variant (SV) data and population frequencies	✅	❌	✅
get_copy_number_variant_info	Retrieve copy number variant (CNV) data and population frequencies	❌	❌	✅
search_for_genes	Search for genes by symbol or name (no direct gene_id lookup in v2/v3)	✅	✅	✅
search_for_variants	Search for variants by ID, gene, or region	✅	✅	✅
get_str_info	Retrieve short tandem repeat (STR) data and population frequencies	❌	❌	✅
get_all_strs	Retrieve all STRs in the dataset	❌	❌	✅
get_variant_liftover	Retrieve liftover mapping for a variant between genomes	✅	❌	❌
get_metadata	Retrieve gnomAD browser metadata and API version info	✅	✅	✅

• ✅ = Supported in this version
• ❌ = Not supported in this version

Dependencies

• Python >= 3.13
• 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
• pytest >= 8.3.5
• pytest-asyncio >= 0.26.0

Directory Structure

.
├── gnomad/              # Main package
│   ├── __init__.py
│   ├── types.py         # Type definitions
│   ├── queries/         # GraphQL query templates
│   │   ├── v2/         # v2.1 specific queries
│   │   ├── v3/         # v3 specific queries
│   │   └── v4/         # v4 specific queries
│   └── schemas/         # Versioned schema files
├── tests/               # Test code and data
│   ├── input/          # Test input data
│   │   ├── analyzed_schemas/  # Analyzed schema data
│   │   ├── schema2query/     # Schema to query conversion
│   │   └── schemas/          # Raw schema files
│   ├── output/         # Test output data
│   │   ├── server/     # Server test outputs
│   │   ├── v2/         # v2.1 test outputs
│   │   ├── v3/         # v3 test outputs
│   │   └── v4/         # v4 test outputs
│   ├── scripts/        # Test utility scripts
│   └── tests/          # Additional test modules
├── server.py           # FastMCP server entrypoint
├── pyproject.toml      # Project metadata
├── README.md           # This file
└── README_tests.md     # Testing documentation

Setup

Install dependencies

uv sync

Activate the virtual environment

. .venv/bin/activate

Test the server

uv --directory ./ run mcp dev server.py

Add the MCP server to your MCP server list (Claude, Cursor, etc.)

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

Run tests

Please see README_tests.md

Query & API Design

• Uses the QueryTemplateEngine pattern to manage version-specific GraphQL query templates.
• Currently, queries are fixed; see (./gnomad/queries)
  • The queries were obtained using schema_fetcher.py and schema_analyzer.py
  • TODO: Dynamic queries
• MCP tool endpoints are documented with detailed parameter and output descriptions.

License

This MCP server itself is licensed under the Apache License 2.0 - see the LICENSE file for details.

This project uses the gnomAD API. Please ensure you cite gnomAD when using this tool or its outputs.

Acknowledgements

• gnomAD
• FastMCP