/folklore-variant-evidence

name: folklore-variant-evidence
description: "Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Use when a scientific agent must branch deterministically on resolved, ambiguous, not-found, invalid, unsupported, or unavailable variant outcomes; chain a resolved public variant into related literature or publication details; or preserve evidence provenance without accepting patient, phenotype, family, segregation, or private case data."
license: MIT
compatibility: Requires network access to api.helena.bio (stateless Streamable HTTP MCP, no credentials); works from any MCP-capable host or via JSON-RPC POST with curl.
metadata:
  version: "1.0"
  skill-author: "Helena Bioinformatics"
  website: "https://folklore.helena.bio"
  github: "https://github.com/helena-bioinformatics/folklore-mcp"

Folklore Variant Evidence

Use Folklore Clinical Variant Interpretation MCP to retrieve structured public variant evidence, automated variant-level ACMG/AMP decision support, provenance, and source-linked literature for professional review. Keep the workflow limited to public identifiers and preserve every explicit outcome state. Adapter 1.5.0 also provides ClinGen Gene-Disease Validity assertions; source coverage is bounded, not every known association.

Folklore Clinical Variant Interpretation MCP is published by Helena Bioinformatics. Its hosted endpoint is:

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

No account or API key is required. The public Apache-2.0 adapter and contract are available at <https://github.com/helena-bioinformatics/folklore-mcp>.

Minimal connection example

A host without native MCP support can make the same public JSON-RPC call:

curl --silent --show-error --fail-with-body --max-time 60 \
  -X POST https://api.helena.bio/folklore/v1/mcp \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json, text/event-stream' \
  -H 'MCP-Protocol-Version: 2026-07-28' \
  -H 'Mcp-Method: tools/call' \
  -H 'Mcp-Name: search_variant_evidence' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"_meta":{"io.modelcontextprotocol/protocolVersion":"2026-07-28","io.modelcontextprotocol/clientCapabilities":{}},"name":"search_variant_evidence","arguments":{"assembly":"GRCh38","query":"rs80357914"}}}'

Inspect the returned outcome before continuing. This example can return `ambiguous` with multiple candidates: stop and request an unambiguous public variant notation instead of selecting a candidate automatically.

Select the right skill

Use this skill when the task is one public variant to structured Folklore evidence, explicit resolution-state handling, variant-linked literature, or ClinGen gene-to-disease/disease-to-gene assertions.

• Use `database-lookup` for broad direct queries across ClinVar, dbSNP, gnomAD,

Ensembl VEP, COSMIC, or multiple databases.

• Use `genomic-coordinates` first when the assembly, coordinate convention,

contig name, or variant representation is uncertain.

• Do not use this skill for VCF annotation, batch processing, somatic variants,

structural variants, polygenic scores, or patient-specific interpretation.

Folklore Clinical Variant Interpretation MCP complements those skills with one source-linked public evidence contract. It does not replace direct database review or qualified clinical judgment.

Enforce the input boundary

Before a variant tool call:

1. Extract exactly one public variant identifier or notation. 2. Require GRCh38 and a germline nuclear SNV or simple indel. 3. Remove or refuse patient names, case identifiers, phenotypes, family history, segregation evidence, clinical records, uploaded files, and other private or patient-specific context. 4. If the task depends on patient context, stop and explain that Folklore Clinical Variant Interpretation MCP does not accept or evaluate it. 5. Never transform a patient-specific request into a public variant query while implying that the result answers the patient-specific question.

Accepted public variant forms include genomic coordinates, genomic/coding/ protein HGVS, SPDI, rsID, or a `canonical_key` returned by Folklore Clinical Variant Interpretation MCP.

Verify the live tool catalog

Connect to the hosted endpoint and call `tools/list`. Verify the available tools instead of relying on model memory. The documented public catalog contains:

• `search_variant_evidence`
• `search_variant_literature`
• `get_publication_details`
• `search_literature_corpus`
• `get_gene_disease_associations`
• `search_disease_genes`

The separate seventh tool `support_helena` is not scientific evidence; use it only when explicitly requested.

If discovery or a tool call fails, preserve the failure as an availability problem. Do not reinterpret it as lack of scientific evidence.

Read [the public MCP contract](references/mcp-contract.md) before composing tool calls or interpreting response states.

Retrieve gene-disease assertions

Use `get_gene_disease_associations` for one exact gene symbol or HGNC identifier, or `search_disease_genes` for an exact MONDO identifier or public disease-name substring. Both accept `limit` (default 20, 1–50) and `offset` (default 0, 0–1000). See the reference for request examples. This is a separate source lookup and requires no variant input or assembly.

Preserve each returned disease identity, inheritance, evidence assessment, source URL, date and snapshot. Do not combine distinct diseases or silently choose among name matches. Gene-disease validity does not classify a particular variant. Empty results mean no matching assertion in the available ClinGen source, not no association. No patient, phenotype, family, segregation, private case data or sequencing files may be sent. Qualified professional review remains requir