gnomad-genetics-mcp-server

gnomad-genetics-mcp-server: get coverage

gnomad_get_coverage

Read-onlyIdempotent

Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input Schema

TableJSON Schema

Name	Required	Description
`gene`	No	Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.
`region`	No	Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id.
`dataset`	No	gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
`transcript_id`	No	Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.
`coverage_source`	No	Restrict to one coverage track. Omit to return every available track.
`reference_genome`	No	Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Guidance when no coverage data is available for the target.
`target`	No	The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes.
`dataset`	No	Effective gnomAD dataset.
`summaries`	No	Per-track coverage summaries (exome and/or genome).
`target_kind`	No	Which target type was queried.
`reference_genome`	No	Effective reference build.

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedSep 30, 2026

changedInput schema / properties / gene / description

Previous value: -"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mutually exclusive with transcript_id and region; blank means omitted."New value: +"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."

changedInput schema / properties / region / anyOf

Previous value: -[
-  {
-    "const": "",
-    "type": "string"
-  },
-  {
-    "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852).",
-    "pattern": "^[0-9XYM]+-\\d+-\\d+$",
-    "type": "string"
-  }
-]New value: +[
+  {
+    "const": "",
+    "type": "string"
+  },
+  {
+    "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1–22, X, or Y, optional chr prefix.",
+    "pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
+    "type": "string"
+  }
+]

changedInput schema / properties / region / description

Previous value: -"Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852). Mutually exclusive with gene and transcript_id."New value: +"Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_target`: Not exactly one of gene, transcript_id, or region was supplied. `incoherent_build`: reference_genome was supplied but does not match the dataset. `invalid_region`: The region names a chromosome outside 1–22, X, Y, or breaks the coordinate bounds. `region_too_large`: The region spans 2,500,000 bp or more, beyond what gnomAD summarizes at once. `mitochondrial_unsupported`: The gene, transcript, or region is on the mitochondrial chromosome (M or MT). `graphql_error`: gnomAD rejected the coverage query with a GraphQL error. `upstream_unavailable`: gnomAD stayed unavailable or throttled through every retry. `upstream_timeout`: Every attempt to reach gnomAD timed out. `upstream_access`: gnomAD refused the request (access denied). `invalid_upstream_response`: gnomAD kept answering with a response that failed validation. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "invalid_target",
-  "incoherent_build"
-]New value: +[
+  "invalid_target",
+  "incoherent_build",
+  "invalid_region",
+  "region_too_large",
+  "mitochondrial_unsupported",
+  "graphql_error",
+  "upstream_unavailable",
+  "upstream_timeout",
+  "upstream_access",
+  "invalid_upstream_response"
+]

Changed5 schema fields changedSep 24, 2026

addedInput schema / properties / gene / anyOf

Added value: +[
+  {
+    "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.",
+    "minLength": 2,
+    "type": "string"
+  },
+  {
+    "description": "Blank — the gene is treated as omitted.",
+    "maxLength": 0,
+    "type": "string"
+  }
+]

changedInput schema / properties / gene / description

Previous value: -"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."New value: +"Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mutually exclusive with transcript_id and region; blank means omitted."

removedInput schema / properties / gene / minLength
```
Removed value: -2
```
removedInput schema / properties / gene / type
```
Removed value: -"string"
```

changedInput schema / properties / transcript_id / description

Previous value: -"Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region."New value: +"Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted."

Changed22 schema fields changedSep 20, 2026
- removedOutput schema / properties / summaries / items / properties / fraction_over_1 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_1 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_10 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_10 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_100 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_100 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_15 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_15 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_20 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_20 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_25 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_25 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_30 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_30 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_5 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_5 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / fraction_over_50 / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / fraction_over_50 / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / mean_depth / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / mean_depth / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / summaries / items / properties / median_depth / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / summaries / items / properties / median_depth / type
```
Added value: +[
+  "number",
+  "null"
+]
```
First observedAug 22, 2026

TDQS

A4.4/5.0

Behavior4/5

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

Annotations already declare readOnly/idempotent/openWorld safety profile, so the burden is lower, yet the description adds real behavior: default returns both tracks, coverage_source narrows to one, and the effective dataset/build are echoed. The mutual-exclusivity and rejection-on-mismatch rules further help the agent predict outcomes.

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?

Information is front-loaded: purpose, output shape, then the disambiguation rationale, then parameter rules. Slightly verbose with some restatement (dataset/build echoing appears twice and the data-source URL), but each sentence carries usable signal.

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?

An output schema exists, so return values need not be explained; combined with 100% schema coverage and the annotations, the description supplies everything an agent needs — purpose, use case, selection constraint, and defaults — for this moderately complex tool.

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

Parameters4/5

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

Schema coverage is 100% so the baseline is 3, but the description adds the selection rule ('supply exactly one of gene, transcript_id, or region') and the default-vs-narrow behavior of coverage_source, reinforcing the key invocation constraint beyond the raw property descriptions.

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 a specific verb and resource ('Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region') and enumerates the returned quantities (mean/median read depth, fraction covered at 1×–100×, split by exome/genome). It is clearly distinguishable from siblings like get_variant or get_gene_constraint.

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?

Gives an explicit motivating use case — 'disambiguate a true absent variant from an uncallable position' — with the reasoning spelled out. It does not name a sibling tool or state when-not-to-use, so it stops short of the 5 tier.

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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