Folklore Clinical Variant Interpretation MCP server

Folklore Clinical Variant Interpretation MCP

Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.

Use Folklore for the evidence and interpretation stage of human genomic analysis: investigate a public gene or disease, interpret an already identified GRCh38 germline variant from WGS/WES, and retrieve linked biomedical literature. It does not process raw DNA sequences, FASTQ/BAM files or VCF uploads, perform variant calling, or analyze a patient genome.

Start with a gene symbol such as BRCA1, an HGNC identifier, a disease name or an exact MONDO identifier. The gene-disease guide documents the two new read-only tools and the ClinGen Gene-Disease Validity coverage boundary.

"What does NM007294.4:c.6869del mean?" and "Review this VUS" are direct entry points. Call searchvariantevidence with one public variant:

{"name":"search_variant_evidence","arguments":{"assembly":"GRCh38","query":"NM_007294.4:c.68_69del"}}

Connect the endpoint below in your MCP client before calling the tool. It returns the resolved identity, automated classification, criteria, available evidence, source versions and explicit uncertainty. See eight observed task workflows and the worked examples.

Already have a ClinVar or Ensembl record? Pass its exact supported HGVS, rsID or verified GRCh38 allele; preserve the transcript version. Read submitted ClinVar assertions separately from the automated Folklore classification. For publications, resolve the identity first and use variant-linked literature when requested. A literature association does not establish pathogenicity.

Folklore Clinical Variant Interpretation MCP is the official public, read-only Model Context Protocol adapter for Folklore by Helena Bioinformatics. It accepts no patient, phenotype, family, segregation or private case context. Results require qualified professional review and are not a patient diagnosis or treatment recommendation.

Connect to the hosted server

No account or API key is required:

https://api.helena.bio/folklore/v1/mcp

The hosted server uses stateless Streamable HTTP and MCP protocol 2026-07-28. Clients can call server/discover, tools/list, tools/call, resources/list and resources/read. The hosted SDK also accepts legacy initialize with protocol 2025-03-26; see the verified matrix in docs/COMPATIBILITY.md. Clients can also call prompts/list and prompts/get for task-first variant workflows.

Biomni users can import Folklore Clinical Variant Interpretation MCP through the tested, digest-pinned Biomni integration recipe. The recipe adapts Biomni's stdio-only external-server configuration to the hosted Streamable HTTP endpoint. Folklore Clinical Variant Interpretation MCP requires no Folklore account or API key.

Biorouter users can build and install the Biorouter BRXT extension. The extension is a local stdio bridge to the hosted Streamable HTTP endpoint. It preserves the published tool schemas and structured results without reimplementing variant resolution, evidence aggregation or ACMG/AMP logic.

Shortened. The full README is on GitHub.