Folklore Clinical Variant Interpretation MCP

Classify or interpret a germline variant under ACMG/AMP

search_variant_evidence

Read-onlyIdempotent

Interpret this variant, explain what this HGVS means, or review this VUS. Use for human genomic variant analysis within bioinformatics workflows, including review of an already identified WGS/WES variant. Use when a user asks to classify or interpret pathogenicity, review a VUS, check available ClinVar assertions or population-frequency evidence, or resolve a variant notation. Classify, interpret or resolve one public GRCh38 germline SNV or simple indel smaller than 50 bp. Accepts coordinates, genomic/coding/protein HGVS, SPDI or rsID. Returns normalized variant identity, automated ACMG/AMP decision support, evidence, provenance and explicit limitations. This is variant-level decision support for professional review. It does not evaluate patient context and must not be presented as a diagnosis or treatment recommendation. Never choose a candidate when resolution is ambiguous.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`query`	Yes	One germline nuclear SNV or simple indel to resolve and interpret; accepted forms include coordinates, genomic/coding/protein HGVS, SPDI, rsID, or a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.
`assembly`	No	Reference genome assembly. Folklore currently accepts GRCh38 only.	GRCh38

Output Schema

TableJSON Schema

Name	Required	Description	Default
`result`	Yes
`record_url`	Yes
`adapter_error`	Yes
`usage_boundary`	Yes
`contract_version`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedAug 25, 2026

addedInput schema / properties / assembly / description

Added value: +"Reference genome assembly. Folklore currently accepts GRCh38 only."

addedInput schema / properties / query / description

Added value: +"One germline nuclear SNV or simple indel to resolve and interpret; accepted forms include coordinates, genomic/coding/protein HGVS, SPDI, rsID, or a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form."

Changed2 schema fields changedAug 11, 2026

addedOutput schema / properties / usage_boundary

Added value: +{
+  "additionalProperties": false,
+  "properties": {
+    "intended_use": {
+      "const": "professional_variant_review",
+      "type": "string"
+    },
+    "not_for": {
+      "items": {
+        "enum": [
+          "patient_diagnosis",
+          "treatment_decision",
+          "standalone_clinical_reporting"
+        ],
+        "type": "string"
+      },
+      "maxItems": 3,
+      "minItems": 3,
+      "type": "array",
+      "uniqueItems": true
+    },
+    "patient_context_evaluated": {
+      "const": false,
+      "type": "boolean"
+    },
+    "result_type": {
+      "const": "automated_variant_level_classification",
+      "type": "string"
+    },
+    "review_required": {
+      "const": true,
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "result_type",
+    "review_required",
+    "patient_context_evaluated",
+    "intended_use",
+    "not_for"
+  ],
+  "type": "object"
+}

changedOutput schema / required

Previous value: -[
-  "contract_version",
-  "record_url",
-  "result",
-  "adapter_error"
-]New value: +[
+  "contract_version",
+  "record_url",
+  "result",
+  "usage_boundary",
+  "adapter_error"
+]

First observedAug 10, 2026

TDQS

A4.2/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already cover readOnly/idempotent/openWorld=false, but the description adds real context: it returns normalized identity, ACMG/AMP decision support, evidence, provenance and limitations, is not a diagnosis, and never selects a candidate when resolution is ambiguous. This ambiguity and limitation disclosure goes beyond the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded with the core action and structured logically, but there is visible redundancy between the opening ('Interpret this variant... review this VUS') and the later 'Use when...' sentence restating classify/interpret/review a VUS.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite an output schema existing, the description fully frames scope, accepted inputs, what is returned, and explicit limitations (no patient context, not a diagnosis). An agent has everything needed to invoke and interpret it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, and the schema already documents accepted input forms (coordinates, HGVS, SPDI, rsID, canonical_key). The description largely restates these forms plus the <50bp and single-variant constraints, adding marginal value over the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States specific verbs (classify, interpret, resolve) and a precise resource and scope: 'one public GRCh38 germline SNV or simple indel smaller than 50 bp.' This clearly separates it from literature-focused siblings like search_variant_literature and search_literature_corpus.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Enumerates concrete when-to-use triggers: classify/interpret pathogenicity, review a VUS, check ClinVar or population-frequency evidence, resolve notation. It does not explicitly name sibling alternatives or state when NOT to use this tool, so it stops short of a 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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