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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

Examples:

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

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.