Folklore Variant Evidence

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"}}}'

The routing headers must match the JSON-RPC method and tool name. A successful HTTP response is not sufficient: inspect JSON-RPC error, then result.structuredContent.adapter_error, then this tool's result.structuredContent.result.status. Other tools use different response shapes; use the contract table.

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 insertion/deletion shorter than 50 base pairs. An unsupported assembly may be rejected by the input schema before any scientific unsupported status exists.
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 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, source.version and source.snapshotSha256. This is a local ClinGen snapshot, not a guarantee of the latest ClinGen release. Follow pagination.nextOffset while it is present; preserve pagination-ceiling warnings. An empty page after the total has been passed does not mean the initial query had no matches. Do not combine distinct diseases or silently choose among name matches. Gene-disease validity does not classify a particular variant. A not_found response means no matching assertion in the available 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 search_variant_evidence 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

Read transport/JSON-RPC errors and adapter_error first. For search_variant_evidence, let envelope = result.structuredContent; only if envelope.result is non-null, branch on envelope.result.status. An invalid_arguments adapter error is distinct from scientific invalid_request. Preserve isError and any typed failure, including resolution_unavailable. Treat the status as a control-flow value, not prose:

Only a resolved result may proceed automatically into a variant-linked literature workflow. Its canonical key is envelope.result.identity.canonical_key. If envelope.result.interpretation.status is unavailable, preserve its typed error; identity resolution has succeeded, but classification has not. Do not read or invent a classification for that outcome.