About Gnomad Link
Gnomad Link is an MCP server in the RAG category: mCP server for gnomAD (Genome Aggregation Database): variant allele frequencies, gene constraint, coverage, structural and mitochondrial variants, and liftover — as typed tools for LLM agents.
Install
git clone https://github.com/berntpopp/gnomad-linkThis 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 (22)
compare_variant_across_datasetsCompare one variant's allele frequencies across gnomAD releases
Parameters not published.
compute_carrier_frequencyCarrier frequency from a single variant (AR / AD / X-linked)
Parameters not published.
compute_gene_carrier_frequencyGene-level recessive carrier rate across qualifying variants
Parameters not published.
compute_variant_liftoverConvert a variant id between GRCh37 and GRCh38
Parameters not published.
get_clinvar_metaClinVar release metadata (deprecated; use `get_server_capabilities`)
Parameters not published.
get_clinvar_variant_detailsClinVar significance, review status, gold stars, submissions
Parameters not published.
get_coverageRead-depth coverage over a gene, region, or variant
Parameters not published.
get_diagnosticsRecent errors, schema drift, and upstream health
Parameters not published.
get_gene_detailsGene constraint metrics (pLI, o/e LoF) and canonical transcript
Parameters not published.
get_gene_summaryOne-shot gene dossier: constraint, transcripts, top ClinVar, expression
Parameters not published.
Show all 22 tools
get_gene_variantsPer-variant rows within a gene, filtered and capped
Parameters not published.
get_mitochondrial_variantMitochondrial variant record, with heteroplasmy
Parameters not published.
get_regionGenes and ClinVar variants in a genomic region
Parameters not published.
get_server_capabilitiesTools, datasets, population codes, live ClinVar release, limits
Parameters not published.
get_structural_variantStructural variant record by id
Parameters not published.
get_transcript_detailsExon structure plus a compact GTEx tissue-expression summary
Parameters not published.
get_variant_detailsFull variant annotation: consequences, predictors, ClinVar
Parameters not published.
get_variant_frequenciesAllele counts and frequencies per population for a variant
Parameters not published.
resolve_variant_idResolve an rsID, partial coordinate, or loose text to a canonical variant id
Parameters not published.
search_genesFind genes by symbol, alias, or Ensembl id
Parameters not published.
search_structural_variantsStructural variants overlapping a gene or region
Parameters not published.
search_variantsDeprecated alias for `resolve_variant_id`
Parameters not published.
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