io.github.cyanheads/gnomad-genetics-mcp-server · v0.4.1 · ai-and-media
io.github.cyanheads/gnomad-genetics-mcp-server is healthy: it completed an MCP handshake in 216 ms and exposes 7 tools.
Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar.
Endpoint: https://gnomad-genetics.caseyjhand.com/mcp (streamable-http)
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| Users (last 30 days) | 0 |
| Handshake | Healthy |
| Auth needed | None |
| Tool count | 7 |
| Latency | 216 ms |
| Last checked (UTC) | 2026-10-16T07:20:34.181Z |
| Checked (UTC) | Status | Latency | Error |
|---|---|---|---|
| 2026-10-16T07:20:34.181Z | Healthy | 216 | |
| 2026-10-15T03:25:36.517Z | Healthy | 3271 |
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. |