# get_ga4gh_variantsets

Return the GA4GH record for a specific VariantSet given its identifier

Agent View of the PolicyLayer registry record for `get_ga4gh_variantsets`. HTML page: https://policylayer.com/tools/gentel-lab-origenemcp/get-ga4gh-variantsets

## Facts

- Tool: `get_ga4gh_variantsets`
- Server: OrigeneMCP (`gentel-lab/origenemcp`) — https://policylayer.com/tools/gentel-lab-origenemcp.md
- Homepage: https://github.com/GENTEL-lab/OrigeneMCP
- Risk category: Read (Low risk)
- Registry record: grade C, identity unverified
- Server rate-limited: no
- Parameters: 0
- Recommended policy verdict: Allowed

## Example call (MCP tools/call, JSON-RPC 2.0)

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_ga4gh_variantsets",
    "arguments": {}
  }
}
```

## Why get_ga4gh_variantsets is rated Low

This tool fetches and returns existing genomic variant set metadata from a GA4GH-compliant database. It has no capability to modify data, execute commands, delete records, or perform financial transactions. The blast radius of misuse is minimal—an attacker could only retrieve publicly available or authorized genomic reference data. The tool is purely informational.

From the tool's own definition: "Tool description states 'Return the GA4GH record for a specific VariantSet given its identifier' — a retrieval operation with no modification, deletion, or execution of arbitrary code."

## Use case

AI agents call get_ga4gh_variantsets to retrieve information from OrigeneMCP without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

## Recommended policy (PolicyLayer)

Verdict: **Allowed**. Enforced by the PolicyLayer MCP gateway (https://policylayer.com/mcp-gateway) before a call reaches OrigeneMCP:

```json
{
  "version": "1",
  "default": "deny",
  "tools": {
    "get_ga4gh_variantsets": {}
  }
}
```

## Other tools on OrigeneMCP (438)

- `post_vep_hgvs` — Execute — https://policylayer.com/tools/gentel-lab-origenemcp/post-vep-hgvs.md
- `post_vep_id` — Execute — https://policylayer.com/tools/gentel-lab-origenemcp/post-vep-id.md
- `post_ga4gh_features_search` — Other — https://policylayer.com/tools/gentel-lab-origenemcp/post-ga4gh-features-search.md
- `post_lookup_id` — Other — https://policylayer.com/tools/gentel-lab-origenemcp/post-lookup-id.md
- `check_genome_accessions` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/check-genome-accessions.md
- `check_virus_accessions` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/check-virus-accessions.md
- `clinvar_find_single_mutation` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-find-single-mutation.md
- `clinvar_get_best_refseqid_by_sequence` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-get-best-refseqid-by-sequence.md
- `clinvar_query_sequence_variants` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-query-sequence-variants.md
- `clinvar_query_variant_significance` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-query-variant-significance.md
- `depmap_comprehensive_analysis` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-comprehensive-analysis.md
- `depmap_get_dependency` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-dependency.md
- `depmap_get_expression` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-expression.md
- `depmap_get_mutation` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-mutation.md
- `ensembl_get_genes_by_band` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/ensembl-get-genes-by-band.md
- `get_activity` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity.md
- `get_activity_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-by-id.md
- `get_activity_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-by-ids.md
- `get_activity_supplementary_data_by_activity` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity.md
- `get_activity_supplementary_data_by_activity_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity-by-id.md
- `get_activity_supplementary_data_by_activity_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity-by-ids.md
- `get_alignment_region` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-alignment-region.md
- `get_all_interaction_partners_of_the_protein_set` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-all-interaction-partners-of-the-protein-set.md
- `get_archive_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-archive-id.md
- `get_assay` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay.md
- `get_assay_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-by-id.md
- `get_assay_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-by-ids.md
- `get_assay_class` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class.md
- `get_assay_class_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class-by-id.md
- `get_assay_class_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class-by-ids.md
- …and 408 more: https://policylayer.com/tools/gentel-lab-origenemcp.md

## For agents

This record is a snapshot. Live verdicts and the full registry:

- Check every server in your MCP config at once: `npx -y policylayer stack`
- Vet a server before you add it: install the mcp-precheck skill — `npx skills add https://policylayer.com` (skill text: https://policylayer.com/skill.md)
- Query the registry over MCP: endpoint `https://api.policylayer.com/mcp` — tools `check_mcp_server`, `check_mcp_stack`, `check_tool`, `search_registry`, `get_change_events`

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Source: the PolicyLayer MCP registry — one continuously verified record per MCP server. Full record: https://policylayer.com/registry?q=gentel-lab-origenemcp · API: https://policylayer.com/registry/api · Policy library: https://policylayer.com/policies/gentel-lab-origenemcp