# gnomad-genetics-mcp-server [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/cyanheads/gnomad-genetics-mcp-server  
**GitHub Stars:** 1  
**npm Downloads (last month):** 1396  
**Views:** 1  
**Installs:** 0  
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**Directory Page:** https://allmcps.com/mcp/gnomad-genetics-mcp-server

## Description
Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.

## Tools
Capabilities this server exposes over MCP:

- **gnomad_get_variant** — Full population record for one or more variants — AC/AN/AF overall and per genetic-ancestry group, homozygote/hemizygote counts, quality flags, per-callset counts and QC status, transcript consequence, in-silico predictors, and joined ClinVar significance.
- **gnomad_get_gene_constraint** — Gene loss-of-function constraint — pLI, LOEUF (`oe_lof_upper`) with confidence interval, observed/expected ratios, and Z-scores. By HGNC symbol or Ensembl gene ID.
- **gnomad_list_gene_variants** — Every variant in a gene, transcript, or region with allele frequencies, predicted consequences, and QC status, filterable by consequence class, max allele frequency, and QC pass, paged by offset.
- **gnomad_get_coverage** — Sequencing coverage across a gene, transcript, or region — mean/median depth and the fraction of samples over depth thresholds, per callset track.
- **gnomad_search_clinvar** — Gene-level ClinVar detail via NCBI E-utilities — classified variants, review status, conditions, submission counts, and gnomAD-compatible variant IDs, paged by offset.
- **gnomad_dataframe_query** — Run a read-only SQL `SELECT` across canvas tables staged by the list tools. Listed only while the canvas is on.
- **gnomad_dataframe_describe** — List the tables staged on a canvas and their columns before writing SQL. Listed only while the canvas is on.
- **gnomad_dataframe_drop** — Drop a named table from a canvas to reclaim memory. Opt-in via `GNOMAD_DATAFRAME_DROP_ENABLED=true` — off by default, and listed only while the canvas is on.

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `npx` (confidence: high):

```json
"mcpServers": {
  "gnomad-genetics-mcp-server": {
    "command": "npx",
    "args": ["-y","@cyanheads/gnomad-genetics-mcp-server"]
  }
}
```

## Documentation

## What gnomad-genetics-mcp-server does

gnomad-genetics-mcp-server exposes gnomAD genetics data through MCP, with clinical significance joined from ClinVar using NCBI E-utilities. It supports population-level variant interpretation, gene constraint analysis, variant catalog searches, and coverage checks across genes, transcripts, and genomic regions.

Variant lookups return overall and ancestry-group allele counts, allele numbers, frequencies, homozygote and hemizygote counts, quality information, callset-level data, transcript consequences, in-silico predictions, and ClinVar significance. Gene constraint queries provide pLI, LOEUF with its confidence interval, observed-to-expected ratios, and Z-scores. The server also provides two data resources for individual variant and gene-constraint records, plus a guided `gnomad_variant_triage` prompt that orders population-frequency, gene-constraint, and callability checks.

## How it works

The server can run over STDIO or Streamable HTTP. A public hosted endpoint is available at `https://gnomad-genetics.caseyjhand.com/mcp`, and the package can be launched locally through npm tooling. MCP clients invoke dedicated tools for single-record lookups, filtered lists, coverage analysis, and ClinVar searches.

List operations return analytical row sets rather than stable resource documents. Those results can be staged in a canvas and inspected with `gnomad_dataframe_describe`; `gnomad_dataframe_query` then runs a read-only SQL `SELECT` across the staged tables. An optional drop operation removes a named table to recover canvas memory.

## Setup and configuration

The repository provides installation links for Claude Desktop, Cursor, and VS Code. A local STDIO setup can use the npm package through `npx`, including the package's latest tag, while the hosted Streamable HTTP endpoint can be configured as the MCP server URL. The project also publishes a container image through GitHub Container Registry.

Configuration includes `GNOMAD_MAX_VARIANT_BATCH`, which raises the per-call variant limit, and `GNOMAD_NORMALIZE_IDS`, which enables case-insensitive rsID matching and conversion of colon-separated coordinate identifiers. `GNOMAD_DATAFRAME_DROP_ENABLED=true` enables the canvas table-drop tool; it is disabled by default.

## Tools and capabilities

- `gnomad_get_variant` accepts variant IDs or rsIDs and returns detailed population, callset, consequence, predictor, QC, and ClinVar information. It supports batches of up to 25 IDs by default.
- `gnomad_get_gene_constraint` looks up loss-of-function constraint by HGNC symbol or Ensembl gene ID.
- `gnomad_list_gene_variants` lists variants for a gene, transcript, or region, with consequence, frequency, and QC filters and offset pagination.
- `gnomad_get_coverage` reports mean and median depth plus the fraction of samples above depth thresholds for each callset track.
- `gnomad_search_clinvar` returns gene-level classifications, review status, conditions, submission counts, and compatible gnomAD variant IDs.
- `gnomad_dataframe_describe` and `gnomad_dataframe_query` support schema inspection and read-only SQL over staged results. `gnomad_dataframe_drop` is available only when explicitly enabled.

## Limitations and notes

Upstream-backed tools and resource reads share a fixed 45-second deadline covering queue waits, retries, response bodies, and chained requests. A variant batch shares that deadline across its items, so completed results can remain available while unfinished primary items report an upstream timeout.

Coordinate variant IDs do not carry a genome build. The server can report a possible match on the other build, but it does not rewrite or retry the identifier automatically. Mitochondrial variant IDs are unsupported. ClinVar failure can leave a valid population result available with a null ClinVar value and an availability flag.

The dataframe SQL interface is read-only and depends on tables staged by list tools. Its table-drop operation is opt-in. Dataset behavior also varies: gnomAD R4 provides joint exome-and-genome population views, while older datasets expose carried callset data without joint populations.

_Full upstream README: https://allmcps.com/mcp/gnomad-genetics-mcp-server/readme_