Clinvar Variation Skill

Operating rules

• Use scripts/clinvar_variation.py for all ClinVar and NCBI Variation work.
• The script accepts max_items; for action=search, start around max_items=10.
• For vcv, rcv, scv, and refsnp, omit max_items unless you need to trim nested arrays in the summary.
• Re-run requests in long conversations instead of relying on prior tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.
• If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting large payloads into chat.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return the JSON verbatim only if the user explicitly asks for machine-readable output.
• Use action=search for the Clinical Tables endpoint.
• Use action=vcv|rcv|scv for ClinVar accessions; they resolve through E-utilities db=clinvar. Use action=refsnp for the NCBI Variation RefSNP object.
• action=search queries the Clinical Tables variants index, which has no VCV/RCV/SCV field. Search by gene symbol or HGVS name; look accessions up with vcv/rcv/scv instead.

Input

• Read one JSON object from stdin.
• Required field: action
• Action-specific required fields:
  • search: terms
  • vcv: vcv
  • rcv: rcv
  • scv: scv
  • refsnp: refsnp
• Optional fields: params, max_items, max_depth, timeout_sec, save_raw, raw_output_path

Output

• search returns total, identifiers, display_rows, extra_fields, and truncation metadata.
• vcv|rcv|scv|refsnp return a compact summary and optional top_keys.
• Use raw_output_path when save_raw=true.
• Failures return ok=false with error.code and error.message.

Execution

echo '{"action":"search","terms":"BRCA1","max_items":10}' | python scripts/clinvar_variation.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/clinvar_variation.py.