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Variant

Use variant commands for compact annotation, source-backed interpretation context, and optional predictive and population-genetics sections.

Accepted variant identifiers

BioMCP supports multiple input forms:

  • rsID: rs113488022
  • HGVS genomic: chr7:g.140453136A>T
  • gene-protein form: BRAF V600E, BRAF p.Val600Glu

These exact formats are accepted by biomcp get variant and the exact-ID helper commands.

Search variants

By gene and protein change:

biomcp search variant -g BRAF --hgvsp V600E --limit 5
biomcp search variant -g BRAF --hgvsp p.Val600Glu --limit 5
biomcp search variant BRAF p.Val600Glu --limit 5

By residue alias shorthand:

biomcp search variant "PTPN22 620W" --limit 5

By protein shorthand when gene context is already supplied:

biomcp search variant -g PTPN22 R620W --limit 5

Standalone protein shorthand like R620W returns variant-specific recovery guidance instead of falling back to gene or condition discovery.

By significance:

biomcp search variant -g BRCA1 --significance pathogenic --limit 5

With population and score filters:

biomcp search variant -g BRCA1 --max-frequency 0.01 --min-cadd 20 --limit 5

Get a variant record

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

The default output favors concise, clinically relevant context first. When BioMCP can derive a compact literature-facing alias, variant search rows and detail cards also show Legacy Name, and JSON output includes legacy_name.

Shorthand such as PTPN22 620W or R620W is not treated as an exact variant ID. Use biomcp search variant for those inputs.

Request variant sections

Prediction section:

biomcp get variant "BRAF V600E" predict

ClinVar-focused section:

biomcp get variant rs113488022 clinvar

ClinVar JSON also exposes top_disease when condition aggregation is available, reusing the highest-ranked ClinVar condition row already shown in the section.

Population section:

biomcp get variant "chr7:g.140453136A>T" population

Population JSON exposes additive compact frequency fields: allele_frequency_raw and allele_frequency_percent. Markdown keeps the raw gnomAD AF line and appends the compact percent inline.

CIViC section:

biomcp get variant "BRAF V600E" civic

GWAS section (trait associations from GWAS Catalog):

biomcp get variant rs7903146 gwas

GWAS JSON exposes supporting_pmids as an ordered, deduplicated array when the section loads successfully. null means either the GWAS section was not loaded or GWAS Catalog was temporarily unavailable. In the unavailable case, JSON also includes gwas_unavailable_reason with a source-specific message.

Predictions (aggregated prediction scores):

biomcp get variant "BRAF V600E" predictions

Conservation (GERP, phyloP):

biomcp get variant rs113488022 conservation

COSMIC (somatic mutation data):

biomcp get variant "BRAF V600E" cosmic

CGI (Cancer Genome Interpreter annotations):

biomcp get variant "BRAF V600E" cgi

cBioPortal (frequency data):

biomcp get variant "BRAF V600E" cbioportal

All supported sections:

biomcp get variant rs113488022 all

Helper commands

biomcp variant trials "BRAF V600E"   # search trials mentioning this mutation
biomcp variant articles "BRAF V600E" # search PubMed for this variant
biomcp variant oncokb "BRAF V600E"   # OncoKB lookup (requires ONCOKB_TOKEN)

Search GWAS associations

By gene:

biomcp search gwas -g TCF7L2 --limit 10

By trait:

biomcp search gwas --trait "type 2 diabetes" --limit 10

Trait search uses GWAS Catalog trait endpoints first, then study-association fallback paths when needed.

Optional enrichment

Variant base output may include cBioPortal enrichment when available. OncoKB is accessed explicitly via biomcp variant oncokb "<gene> <variant>" and requires ONCOKB_TOKEN.

Prediction requirements

Prediction sections may require ALPHAGENOME_API_KEY depending on source path. Unsupported inputs are surfaced with explicit validation messages.

JSON mode

biomcp --json get variant "BRAF V600E"
biomcp --json get variant rs7903146 gwas
biomcp --json search gwas --trait "type 2 diabetes"

Practical tips

  • Use search variant first for shorthand or ambiguous inputs.
  • Start with the base card, then add source sections such as clinvar, civic, or population only when needed.
  • Use all when you need a one-shot export for review or downstream comparison.