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How to: annotate variants

BioMCP provides lightweight variant annotation suitable for triage and workflow automation.

Choose an ID format

biomcp get variant supports:

  • rsID: rs113488022
  • HGVS genomic: chr7:g.140453136A>T
  • Gene + protein change: BRAF V600E, BRAF p.Val600Glu

Examples:

biomcp get variant rs113488022
biomcp get variant "chr7:g.140453136A>T"
biomcp get variant "BRAF V600E"
biomcp get variant "BRAF p.Val600Glu"

get variant stays exact-only. If you have shorthand like PTPN22 620W or R620W, resolve it through search variant first.

Search shorthand aliases

biomcp search variant accepts a few common search-only shorthand forms in addition to the exact identifiers above:

  • Gene + residue alias: PTPN22 620W
  • Gene flag + protein shorthand: biomcp search variant -g PTPN22 R620W
  • Long-form protein notation: biomcp search variant -g BRAF --hgvsp p.Val600Glu

Examples:

biomcp search variant "PTPN22 620W" --limit 10
biomcp search variant -g PTPN22 R620W --limit 10
biomcp search variant BRAF p.Val600Glu --limit 10

Standalone protein shorthand like R620W is still too ambiguous to run automatically. BioMCP returns variant-specific guidance instead of silently searching the wrong entity.

Filter search results

biomcp search variant -g BRCA1 --significance pathogenic --limit 10

Add frequency and score filters:

biomcp search variant -g BRCA1 --max-frequency 0.01 --min-cadd 20 --limit 10

Optional enrichments

  • OncoKB (set ONCOKB_TOKEN for the production endpoint)
  • cBioPortal mutation summaries (best-effort)

If these services are unavailable, BioMCP degrades gracefully and will still return core annotations.