folklore-variant-evidence skill

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 .

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.

Ensembl VEP, COSMIC, or multiple databases.

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

contig name, or variant representation is uncertain.

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

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

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

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:

segregation evidence, clinical records, uploaded files, and other private or patient-specific context.

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,

Clinical Variant Interpretation MCP does not accept or evaluate it.

1. If the task depends on patient context, stop and explain that Folklore

implying that the result answers the patient-specific question.

1. Never transform a patient-specific request into a public variant query while

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:

• searchvariantevidence
• searchvariantliterature
• getpublicationdetails
• searchliteraturecorpus
• getgenedisease_associations
• searchdiseasegenes

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 before composing tool calls or interpreting response states.

Retrieve gene-disease assertions

Use getgenediseaseassociations for one exact gene symbol or HGNC identifier, or searchdisease_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 required.

Run the variant-evidence workflow

1. Resolve and retrieve evidence

Call searchvariantevidence with:

assembly: GRCh38
query: <one public variant identifier or notation>

Do not add phenotype, disease, patient, family, or treatment context to this call. Preserve the returned contract fields, source links, limitations, and usage boundary.

2. Branch on the returned status

Treat the status as a control-flow value, not prose:

Only a resolved result may proceed automatically into a variant-linked literature workflow. If a resolved interpretation itself reports unavailable evidence, preserve that separate limitation.

3. Review the evidence without overclaiming

For a resolved result:

as returned.

• Present the returned variant identity and canonical_key.
• Preserve the automated variant-level ACMG/AMP decision-support result exactly

recommendation, or standalone clinical report.

• Cite the returned public sources and provenance.
• Separate returned facts from the agent's synthesis.
• State that qualified professional review is required.
• Do not turn the result into a diagnosis, individual risk estimate, treatment

Chain into literature

Variant-linked literature

After a resolved evidence call, pass the returned canonicalkey to searchvariant_literature. Keep assembly as GRCh38. An optional question may narrow the literature focus, but it must remain a public scientific question and must not contain patient context.

Distinguish each result's match type:

• exact_variant: direct match to the resolved variant
• variant_alias: match through a reported alias
• gene_association: broader gene-level association, not variant-specific proof

Literature associations do not alter the returned ACMG/AMP classification.

Publication details

Call getpublicationdetails only with a PMID returned by the literature tools. Preserve PubMed URLs, DOI/PMCID fields when present, retraction status, and the distinction between gene mentions and variant mentions.

Semantic corpus search

Use searchliteraturecorpus for a public natural-language scientific question or for discovery by publication identifier, gene, variant, phenotype, HPO, or OMIM concept. Treat results as source-linked candidates for professional review. A zero-result response means no result was returned for that bounded query, not that no relevant publication exists anywhere.