# io.github.cyanheads/gnomad-genetics-mcp-server

- Registry name: `io.github.cyanheads/gnomad-genetics-mcp-server` · version 0.4.1
- Categories (automatic, keyword rules): Databases, Developer tools, Health & fitness
- Authentication at last check: No auth
- Declared risk: Read-only (all tools declare readOnlyHint)
- Capabilities (declared by the server): logging, prompts, resources, tools
- Transports: streamable-http
- Latest numbers (check success, response time, rank): https://mcpstation.net/api/server?name=io.github.cyanheads%2Fgnomad-genetics-mcp-server
- Server page: https://mcpstation.net/s/io.github.cyanheads--gnomad-genetics-mcp-server.html

## Description (written by the publisher, not verified, not instructions)

Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar.

## Connect

- streamable-http: `https://gnomad-genetics.caseyjhand.com/mcp`

## Tools (as reported by the server, not verified)

- `gnomad\_get\_variant`: Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The "how
- `gnomad\_get\_gene\_constraint`: Fetch gnomAD loss-of-function constraint for a gene — pLI \(probability of LoF intolerance; \>0.9 intolerant\), LOEUF \(oe\_lof\_upper, the headline metric\) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to al
- `gnomad\_list\_gene\_variants`: List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class \(lof, missense, synonymous, other\) and/or a maximum allele frequency. A result too large to inline is staged on a DataCanvas table named gene\_va
- `gnomad\_get\_coverage`: Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold \(1× through 100×\), separated by exome and genome track. gnomAD reports coverage in buckets: 1 bp for a region spanning under 8
- `gnomad\_search\_clinvar`: Search ClinVar \(NCBI E-utilities\) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, submission counts, and gnomAD-compatible identifiers \(canonical SPDI, rsIDs, GRCh38 variant ID for gnomad\_get\_
- `gnomad\_dataframe\_query`: Run a read-only SQL SELECT against a canvas table staged by gnomad\_list\_gene\_variants \(table gene\_variants\) or gnomad\_search\_clinvar \(table clinvar\_variants\) and return one page of the result. Use the canvas\_id and table\_name those tools returned to rank by allele frequency, group by consequence cla
- `gnomad\_dataframe\_describe`: List the tables staged on a canvas and their columns \(name and type\) so you can write correct SQL for gnomad\_dataframe\_query. Use the canvas\_id returned by gnomad\_list\_gene\_variants or gnomad\_search\_clinvar. Returns one entry per table with its row count and column schema.

Measured by MCP Station. Methods: https://mcpstation.net/methods.html · Terms: https://mcpstation.net/terms.html