{
  "name": "genomics-variants-mcp",
  "title": "HealthMesh · Genomic Variants MCP (gnomAD + ClinVar)",
  "version": "0.1.4",
  "description": "Live human genetic variant lookups: gnomAD population allele frequencies (overall and by genetic ancestry group, exomes/genomes/joint, filters, grpmax/FAF, in-silico predictors, canonical consequence) for variant IDs or rsIDs; gnomAD gene constraint (pLI, LOEUF, missense Z) and gene variant lists filtered by consequence and frequency; ClinVar records (germline classification, review status stars, conditions, somatic impact/oncogenicity) by VCV, variation ID, rsID or HGVS; and ClinVar search by gene, condition, classification and minimum review stars. Research reference only, not for clinical decisions. No key.",
  "healthmesh_domain": "Research, Trials & Genomics",
  "datasets": [
    "RES-04",
    "RES-05"
  ],
  "mcp_endpoint": "https://genomics-variants.healthmesh.ai/mcp",
  "transport": "Streamable HTTP (stateless, JSON responses)",
  "authorization": "none",
  "auth_mode": "off",
  "docs": "https://github.com/HendrikK/healthmesh/tree/main/servers/genomics-variants-mcp#readme",
  "contact": "hendrik.kleine@gmail.com",
  "data_source": {
    "name": "gnomAD GraphQL API (Broad Institute) + NCBI ClinVar via E-utilities",
    "url": "https://gnomad.broadinstitute.org/",
    "license": "gnomAD summary data ODC-ODbL/CC0 (cite gnomAD); ClinVar public domain U.S. Government data; no endorsement implied",
    "refresh": "live (gnomAD 24 h edge cache; ClinVar 6 h, updated weekly)"
  },
  "tools": [
    {
      "name": "gnomad_get_variant",
      "title": "gnomAD variant allele frequencies",
      "description": "Returns gnomAD allele counts and frequencies for 1-10 variants (variant IDs like 1-55051215-G-GA, chr1:55051215:G:GA, or dbSNP rsIDs): combined (v4 joint exome+genome) AC/AN/AF, homozygotes, exome and genome detail with QC filters, per-ancestry-group frequencies, grpmax and FAF95, flags, in-silico predictors (CADD, REVEL, SpliceAI, ...) and the MANE/canonical transcript consequence (HGVS, LOFTEE). rsIDs can map to several alleles; each is returned."
    },
    {
      "name": "gnomad_get_gene_constraint",
      "title": "gnomAD gene constraint (pLI, LOEUF, missense Z)",
      "description": "Returns gnomAD gene constraint metrics for a gene (HGNC symbol or Ensembl ID): observed/expected pLoF (o/e with 90% CI; upper bound = LOEUF), pLI, missense o/e and Z, synonymous Z, and constraint flags. GRCh38 = gnomAD v4.1 constraint (default), GRCh37 = v2.1.1."
    },
    {
      "name": "gnomad_list_gene_variants",
      "title": "gnomAD variants in a gene",
      "description": "Lists gnomAD short variants in a gene with filters: consequence category (lof = pLoF stop/frameshift/essential splice, missense incl. in-frame indels, synonymous, splice_region, other), LOFTEE high-confidence only, PASS only, allele-frequency range; sorted by frequency or position, with counts per category. Large genes are fetched whole from gnomAD (can take several seconds)."
    },
    {
      "name": "clinvar_get_variant",
      "title": "ClinVar record for a variant",
      "description": "Returns ClinVar records for a variant given a VCV accession (VCV000017661), ClinVar variation ID (17661), RCV accession, dbSNP rsID (rs121913529), HGVS expression (NM_004985.5:c.35G>T, any RefSeq transcript/genomic accession) or GRCh38 chrom-pos-ref-alt (12-25245350-C-A; SNVs and indels). HGVS and chrom-pos-ref-alt are normalised to the canonical genomic allele (NCBI Variation Services) for an exact match. Returns: germline classification with review status and stars, last evaluated date, conditions (MedGen/OMIM/MONDO IDs), somatic clinical impact and oncogenicity, genes, protein change, molecular consequence, GRCh38/GRCh37 locations, canonical SPDI, cross-references and submission counts. An rsID or position can return several alleles."
    },
    {
      "name": "clinvar_search",
      "title": "Search ClinVar",
      "description": "Searches ClinVar by gene, condition, classification (pathogenic, likely_pathogenic, pathogenic_or_likely_pathogenic, vus, likely_benign, benign, benign_or_likely_benign, conflicting), minimum review stars (0-4), molecular consequence and variant type. Returns the total count and one row per variant with classification, review status, stars, conditions, protein change and somatic classifications, with paging."
    },
    {
      "name": "genomics_describe_dataset",
      "title": "Describe the gnomAD and ClinVar sources",
      "description": "Explains the gnomAD and ClinVar sources behind this server: versions, reference genomes, population groups, filters, constraint metrics, ClinVar review stars and classifications, update frequency, rate limits and caveats."
    }
  ]
}