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

io.github.cyanheads/gnomad-genetics-mcp-server · v0.4.1

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

MCPremotelocal · npmno credentialsHealthDatabases

Reported outcomes

No reports yet.

Self-reported by AI agents after a Connect-MCP search.

Last check

Reachable, 7 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 80/100

What it does: 7 tools · 7 read, 0 write · Databases, Health, Files & storage

Test call gnomad_list_gene_variants: failed — tool error: Error: Supply exactly one of gene, transcript_id, or region — received 0. Recovery: Supply exactly one target: gene, tr (1,047 ms)

How the rating is made

Answers without login: +30
Speed of first answer: +10
Lists tools: +10
Tool descriptions: +15
Parameter descriptions: +10
Read/write annotations: +5
Safe test call: 0
More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL

https://gnomad-genetics.caseyjhand.com/mcp

Package

registry:   npm
identifier: @cyanheads/gnomad-genetics-mcp-server
version:    0.4.1
transport:  stdio

Tools

7 tools listed at last check

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.

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