Gnomad

Transcript

transcript

Read-onlyIdempotent

Fetch gnomAD variant data for an Ensembl transcript (ENST…), returning transcript coordinates, gene symbol, chromosome position, and per-variant allele counts (ac/an) from exome and genome datasets. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.

Input Schema

Name	Required	Description
`limit`	No	Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset.
`offset`	No	Skip this many variants first, for the next page (variants_page.next_offset). Default 0.
`dataset`	No
`transcript_id`	Yes	Ensembl transcript id (ENST…)

Output Schema

Name	Required	Description
`truncated`	No	True when this response holds fewer variants than gnomAD has (see variants_page)
`transcript`	No
`variants_page`	No	How the variant list was paged. gnomAD returns every variant with no limit of its own, so the pack pages it; total is exact.

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedOct 31, 2026

addedInput schema / properties / limit

Added value: +{
+  "description": "Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset.",
+  "type": "number"
+}

addedInput schema / properties / offset

Added value: +{
+  "description": "Skip this many variants first, for the next page (variants_page.next_offset). Default 0.",
+  "type": "number"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when this response holds fewer variants than gnomAD has (see variants_page)",
+  "type": "boolean"
+}

addedOutput schema / properties / variants_page

Added value: +{
+  "description": "How the variant list was paged. gnomAD returns every variant with no limit of its own, so the pack pages it; total is exact.",
+  "properties": {
+    "limit": {
+      "description": "Page size applied",
+      "type": "number"
+    },
+    "next_offset": {
+      "description": "Offset for the next page, null on the last page",
+      "type": [
+        "number",
+        "null"
+      ]
+    },
+    "note": {
+      "description": "Plain-language statement of what is and is not in this page",
+      "type": "string"
+    },
+    "offset": {
+      "description": "Variants skipped before this page",
+      "type": "number"
+    },
+    "returned": {
+      "description": "Variants in this response",
+      "type": "number"
+    },
+    "total": {
+      "description": "Variants gnomAD holds for this query",
+      "type": "number"
+    },
+    "upstream_bytes": {
+      "description": "Size of the full upstream response, in bytes",
+      "type": "number"
+    }
+  },
+  "type": "object"
+}

Changed2 schema fields changedMay 22, 2026

addedInput schema / examples

Added value: +[
+  {
+    "transcript_id": "ENST00000357144"
+  },
+  {
+    "dataset": "gnomad_r4",
+    "transcript_id": "ENST00000380152"
+  }
+]

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "properties": {
+    "transcript": {
+      "properties": {
+        "chrom": {
+          "description": "Chromosome",
+          "type": "string"
+        },
+        "gene_symbol": {
+          "description": "Gene symbol",
+          "type": "string"
+        },
+        "start": {
+          "description": "Transcript start position",
+          "type": "number"
+        },
+        "stop": {
+          "description": "Transcript stop position",
+          "type": "number"
+        },
+        "transcript_id": {
+          "description": "Ensembl transcript ID",
+          "type": "string"
+        },
+        "variants": {
+          "items": {
+            "properties": {
+              "consequence": {
+                "description": "VEP consequence",
+                "type": "string"
+              },
+              "exome": {
+                "properties": {
+                  "af": {
+                    "description": "Allele frequency",
+                    "type": "number"
+                  }
+                },
+                "type": "object"
+              },
+              "genome": {
+                "properties": {
+                  "af": {
+                    "description": "Allele frequency",
+                    "type": "number"
+                  }
+                },
+                "type": "object"
+              },
+              "variant_id": {
+                "description": "Variant identifier",
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        }
+      },
+      "type": "object"
+    }
+  },
+  "type": "object"
+}

First observedMay 16, 2026

TDQS

A4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint, and non-destructive behavior, so the safety profile is covered. The description adds useful behavioral context about pagination: default 500, max 2,000, and the presence of variants_page totals and next_offset. It does not cover authentication, rate limits, or error behavior, so it stops short of a 5.

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

Conciseness5/5

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

The description is two sentences, front-loaded with the primary purpose and followed by essential paging behavior. Every sentence adds useful information without repetition or filler.

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

Completeness4/5

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

An output schema exists, so the description need not explain return values in full, though it helpfully names the main returned fields. It also covers paging sufficiently for correct invocation. The main gap is the undocumented dataset parameter and the absence of error or limitation behavior, which keeps it from being fully complete.

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 75%, so the baseline is 3. The description reinforces limit/offset paging, but that information is already present in the limit schema description, and the dataset parameter is not given any semantic explanation in either the description or 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?

The description uses a specific verb and resource: 'Fetch gnomAD variant data for an Ensembl transcript (ENST…)'. It also names the returned fields (transcript coordinates, gene symbol, chromosome position, allele counts), which makes the tool clearly distinguishable from generic sibling tools like variant or gene.

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

Usage Guidelines3/5

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

Usage is implied by naming the required Ensembl transcript ID, but the description does not explicitly state when to use this tool instead of siblings such as variant or gene. There are no exclusions or alternative-routing instructions.

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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