MCP server

Gnomad Genetics

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

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Source

At a glance

Type

MCP server

Publisher

Not verified

Status

Working at last check

Tools

7

Token cost

About 4,628 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http gnomad-genetics-mcp-server https://gnomad-genetics.caseyjhand.com/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.gnomad-genetics-mcp-server]
url = "https://gnomad-genetics.caseyjhand.com/mcp"

Gemini CLI

{"mcpServers":{"gnomad-genetics-mcp-server":{"httpUrl":"https://gnomad-genetics.caseyjhand.com/mcp"}}}

Cursor

{"mcpServers":{"gnomad-genetics-mcp-server":{"url":"https://gnomad-genetics.caseyjhand.com/mcp"}}}

VS Code

{"servers":{"gnomad-genetics-mcp-server":{"type":"http","url":"https://gnomad-genetics.caseyjhand.com/mcp"}}}

Antigravity

agy mcp add gnomad-genetics-mcp-server https://gnomad-genetics.caseyjhand.com/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"gnomad-genetics-mcp-server","server_url":"https://gnomad-genetics.caseyjhand.com/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"gnomad-genetics-mcp-server","server_url":"https://gnomad-genetics.caseyjhand.com/mcp"}

Tools

• gnomad_dataframe_describe ~189 tokens
  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.
• gnomad_dataframe_query ~550 tokens
  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_get_coverage ~836 tokens
  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_get_gene_constraint ~583 tokens
  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_get_variant ~579 tokens
  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_list_gene_variants ~1033 tokens
  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_search_clinvar ~858 tokens
  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_

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