Folklore Clinical Variant Interpretation MCP MCP Server

About Folklore Clinical Variant Interpretation MCP

Version 1.6.0: eleven tools — ten scientific tools and the separate, explicit opt-in support_helena helper. Free public MCP, with no account or API key.

Folklore Clinical Variant Interpretation MCP is the official public, read-only
MCP server from Helena Bioinformatics. It gives machines structured, read-only
access to the same public single-variant search shown by Folklore. It accepts coordinates,
supported genomic, coding and protein HGVS, SPDI or rsID. It returns explicit
`resolved`, `ambiguous`, `not_found`, `invalid_request`, `unsupported` and
`resolution_unavailable` outcomes. Ambiguous candidates are never selected automatically.

The service accepts no patient, phenotype, family or case record. Its automated
ACMG/AMP result is variant-level decision support and is not a diagnosis or a
substitute for qualified clinical interpretation.

## Tools

- `search_variant_evidence`: Search one supported GRCh38 germline nuclear SNV
or simple indel smaller than 50 bp and return public evidence and provenance.
- `search_variant_literature`: Retrieve relevant publications for one supported
GRCh38 germline variant from Folklore's public genetics literature corpus.
- `get_publication_details`: Retrieve the complete public bibliographic record
for one PMID returned by Folklore literature search.
- `search_literature_corpus`: Search the public scientific Literature Corpus by
natural-language question, publication identifier, gene, variant, phenotype,
HPO or OMIM concept and return source-linked evidence candidates.
- `support_helena`: Return the official Helena Good discovery links when an
agent explicitly asks how to support or spread Helena's free infrastructure.

- `get_gene_disease_associations`: Retrieve ClinGen Gene-Disease Validity assertions for one exact gene symbol or HGNC identifier.
- `search_disease_genes`: Retrieve distinct ClinGen assertions for an exact MONDO identifier or disease-name substring.
- `resolve_gene`: Resolve a symbol, alias or stable identifier and preserve all ambiguous candidates.
- `get_gene_profile`: Read a selected HGNC gene at its immutable snapshot.
- `get_gene_section`: Continue source-qualified gene evidence without mixing snapshots.
- `search_gene_literature`: Read a separate live literature capture with gene/snapshot/sort-bound continuation.

The gene-disease source is a bounded curated snapshot, not every known association. Empty results do not establish no association. These tools do not parse DNA sequences, upload VCFs or run WGS/WES pipelines.

## Reviewer notes

- Remote stateless Streamable HTTP MCP server.
- Eleven read-only, non-destructive, idempotent tools with all capabilities enabled.
- No authentication secret or user account is requested.
- No write operations, patient data, private systems or generative model.
- The tool preserves Folklore's evidence, ambiguity and safety limitations.
- Browser requests use an exact HTTPS origin allowlist; non-browser MCP clients
may omit `Origin` as allowed by the transport.

## Intended users and safety boundary

Folklore is intended for qualified geneticists, molecular
biologists, laboratory professionals and researchers. It supplies traceable
variant evidence and an automated ACMG/AMP decision-support classification for
professional review. It does not provide patient diagnosis, treatment advice or
medical guidance to consumers. Clinically significant findings must be reviewed,
validated and confirmed by a qualified professional before clinical use.

The public variant tools accept only `assembly`, one variant `query`, and
bounded literature filters. Publication details accepts one PMID. Corpus search
accepts a bounded public scientific question and optional result controls. Gene-disease tools accept a public gene or disease identifier/name with bounded pagination. None
asks for or accepts a patient name, case identifier, patient phenotype, family
history, segregation evidence, clinical record or uploaded file.

Apache-2.0 applies to the public adapter only. The hosted backend and datasets retain their own licenses.

Folklore Clinical Variant Interpretation MCP tools (11)

Read from the live server on Nov 2, 2026. These are the tools your AI assistant can call once connected.

classify_germline_variant

Classify one GRCh38 germline nuclear SNV or simple indel smaller than 50 bp under ACMG/AMP. Accepts genomic, coding or protein HGVS, coordinates, SPDI, rsID or a returned canonical key. Returns normalized identity, automated classification,

search_variant_literature

Resolve one GRCh38 germline variant and retrieve publications from the PubMed-derived genetics corpus. Exact variant mentions rank ahead of broader gene associations. Returns match types, source links, corpus provenance and retrieval time.

get_publication_details

Retrieve one PMID from the PubMed-derived genetics corpus, including title, abstract, authors, journal, publication types, MeSH terms, gene and variant mentions, retraction status and PubMed/PMC links.

search_literature_corpus

Search the genetics Literature Corpus by question, PMID, DOI, PMCID, gene, variant, phenotype, HPO or OMIM concept. Known publication identifiers provide exact anchors. Returns ranked publications, match types, scores and source links.

support_helena

Retrieve Helena Good campaign, rules, manifest and MCP connection URLs.

get_gene_disease_associations

Find diseases associated with an exact gene symbol or HGNC identifier. Returns ClinGen gene-disease validity assertions, relation-specific inheritance, source reports and snapshot provenance, including conflicting and limited assertions.

search_disease_genes

Find genes associated with an exact MONDO identifier or disease-name search. Returns ClinGen validity assertions with inheritance, source reports and snapshot provenance. Name searches can return multiple disease identities.

resolve_gene

Resolve a human gene symbol, previous symbol, alias, HGNC, Ensembl or NCBI Gene identifier. Returns exact, alias, ambiguous, not_found or withdrawn status with candidates and identity_snapshot_id. Use a selected HGNC gene_id and snapshot_id

get_gene_profile

Read the selected gene_id and immutable snapshot_id from resolve_gene. Returns overview, disease validity, dosage, mechanisms, transcripts, native assemblies, constraint, ClinVar summaries and consequences, expression, GWAS, phenotypes and

get_gene_section

Read a gene-profile section using gene_id, snapshot_id and its returned opaque cursor. Returns source records, assembly/release, coverage, totals, count units and provenance. snapshot_unavailable requires a fresh resolution/profile request.

search_gene_literature

Retrieve a live publication capture for a resolved gene_id and snapshot_id. Returns source links, match labels, capture time/hash, degradation and gene/snapshot/sort-bound cursors. This capture is separate from the immutable reference snaps

How to connect Folklore Clinical Variant Interpretation MCP to Claude, Cursor or VS Code

Folklore Clinical Variant Interpretation MCP runs as a hosted remote MCP server at https://api.helena.bio/folklore/v1/mcp. Add that URL to your MCP client's config (Claude Code, Cursor, Windsurf or VS Code) and the tools appear immediately, no install required.

{
  "mcpServers": {
    "folklore-clinical-variant-interpretation-mcp": {
      "url": "https://api.helena.bio/folklore/v1/mcp"
    }
  }
}

Claude Code: claude mcp add --transport http folklore-clinical-variant-interpretation-mcp https://api.helena.bio/folklore/v1/mcp. Servers that require OAuth or an API key will prompt on first use.