Ancestry allele frequencies, LoF constraint, variant lists, and coverage from gnomAD, with ClinVar.
Connect Remote server
claude mcp add --transport http gnomad-genetics-mcp-server https://gnomad-genetics.caseyjhand.com/mcp{
"mcpServers": {
"gnomad-genetics-mcp-server": {
"url": "https://gnomad-genetics.caseyjhand.com/mcp"
}
}
}{
"servers": {
"gnomad-genetics-mcp-server": {
"type": "http",
"url": "https://gnomad-genetics.caseyjhand.com/mcp"
}
}
}Settings > Connectors > Add custom connector
URL: https://gnomad-genetics.caseyjhand.com/mcpTools 8 found in our last check
gnomad_get_variantFetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, the filtering allele frequency (faf95) to test against a disease threshold such as ACMG/AMP BA1 or BS1, homozygote and hemizygote…
gnomad_get_gene_constraintFetch 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 and gnomAD’s LOEUF percentile, observed/expected ratios for LoF, missense, and synonymous variation with 90…
gnomad_list_gene_variantsList every gnomAD variant in a gene, transcript, or region with allele frequencies, filtering allele frequencies, zygosity counts, predicted consequences with LOFTEE's loss-of-function call, and QC status, optionally filtered to one consequence class (lof, missense, synonymous,…
gnomad_get_coverageFetch 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 re…
gnomad_get_variant_cooccurrenceEstimate whether two variants in the same gene sit on different haplotypes (in trans — compound heterozygous) or on the same one (in cis), from gnomAD v2.1 exome genotypes: the probability of compound heterozygosity and the genotype and haplotype counts behind it, overall and pe…
gnomad_search_clinvarSearch ClinVar (NCBI E-utilities) for a gene and return its classified variants — the germline clinical significance with its review status, 0–4 star rating, and conditions; any somatic oncogenicity or clinical-impact classification with its own review status and tumor types; mo…
gnomad_dataframe_queryRun 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, gro…
gnomad_dataframe_describeList 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.
Details
| Endpoint | https://gnomad-genetics.caseyjhand.com/mcp (Streamable HTTP) |
| Package | @cyanheads/[email protected] (NPM, stdio) |
| Package | @cyanheads/[email protected] (NPM, streamable-http) |
| First published | 4 Nov 2026 |
| Last updated | 4 Nov 2026 |
| Registry name | io.github.cyanheads/gnomad-genetics-mcp-server |
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