Gnomad MCP Server

shukwong/gnomad-mcp-server

A Model Context Protocol (MCP) server that provides access to the gnomAD (Genome Aggregation Database) GraphQL API. This server enables AI assistants to query genetic variant data, gene constraints, and population genetics information from gnomAD.

View on GitHub

Install

npx @modelcontextprotocol/cli gnomad-mcp-server

Client configuration

{
  "mcpServers": {
    "gnomad": {
      "command": "node",
      "args": [
        "/path/to/gnomad-mcp-server/dist/index.js"
      ]
    }
  }
}

Author: @shukwong
Category: Research & Data, Developer Tools
Updated: Oct 6, 2026

Features

Gene Information: Search and retrieve detailed gene data including constraint scores
Variant Analysis: Query specific variants and their population frequencies
Population Genetics: Access allele frequencies across different populations
Constraint Scores: Get pLI, LOEUF, and other constraint metrics
Region Queries: Find variants within specific genomic regions
Transcript Data: Access transcript-specific information and constraints
Coverage Data: Retrieve sequencing coverage statistics
Structural Variants: Query structural variant data
Mitochondrial Variants: Access mitochondrial genome variants

Tools (4)

reference_genome
Reference genome (GRCh37 or GRCh38, default: GRCh38)
dataset
Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc., default: gnomad_r4)
get_gene
Get detailed information about a gene including constraint scores.
get_variant
Get detailed information about a specific variant.

Details on this page are taken from the project's README. Open README

Supported clients

Clients mentioned in this server's README:

View all

Claude Desktop

Desktop · Freemium · Proprietary

Anthropic's official Claude AI desktop application. Supports MCP servers to extend functionality.

WindowsMacOS

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