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MCP server · RAG

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

· github.com/cyanheads/gnomad-genetics-mcp-server

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

Unclaimed rag
InstallView source
37Low

Scored 3 months ago · breakdown

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

io.github.cyanheads/gnomad-genetics-mcp-server is an MCP server in the RAG category: look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.

Install

Claude Code
claude mcp add io-github-cyanheads-gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server
npx
npx -y @cyanheads/gnomad-genetics-mcp-server

This server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.

Tools (8)

gnomad_dataframe_describeList the tables staged on a canvas and their columns before writing SQL.

Parameters not published.

gnomad_dataframe_dropDrop a named table from a canvas to reclaim memory. Opt-in via `GNOMAD_DATAFRAME_DROP_ENABLED=true` — off by default since per-table TTL already handles cleanup.

Parameters not published.

gnomad_dataframe_queryRun a read-only SQL `SELECT` across canvas tables staged by the list tools.

Parameters not published.

gnomad_get_coverageSequencing coverage across a gene, transcript, or region — mean/median depth and the fraction of samples over depth thresholds, per callset track. Tells a true absent variant from an uncallable position.

Parameters not published.

gnomad_get_gene_constraintGene loss-of-function constraint — pLI, LOEUF (`oe_lof_upper`) with CI, observed/expected ratios, and Z-scores. By HGNC symbol or Ensembl gene ID.

Parameters not published.

gnomad_get_variantFull population record for one or more variants — AC/AN/AF overall and per genetic-ancestry group, homozygote/hemizygote counts, quality flags, transcript consequence, in-silico predictors, and joined ClinVar significance. Batch up to 25 IDs with per-item partial success.

Parameters not published.

gnomad_list_gene_variantsEvery variant in a gene, transcript, or region with allele frequencies and predicted consequences, filterable by consequence class and max AF. Spills to the `gene_variants` canvas table.

Parameters not published.

gnomad_search_clinvarGene-level ClinVar detail via NCBI E-utilities — classified variants, review status (star rating), conditions, and submission counts. Spills to the `clinvar_variants` canvas table.

Parameters not published.

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Questions

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

How do I install io.github.cyanheads/gnomad-genetics-mcp-server?

Run claude mcp add io-github-cyanheads-gnomad-genetics-mcp-server -- npx -y @cyanheads/gnomad-genetics-mcp-server, then add the server to your MCP client's configuration.

Is io.github.cyanheads/gnomad-genetics-mcp-server safe to use with an AI agent?

Its trust score is 37 out of 100 (low). Conduid hasn't run static security checks on this repository yet, so review the source yourself before granting it credentials. It has no ConduID identity yet, so agent calls to it are not receipted.

Is io.github.cyanheads/gnomad-genetics-mcp-server still maintained?

Conduid hasn't recorded a commit date for this repository yet. Check the repository directly for recent activity.