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

Get a variant record¶

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

The default output favors concise, clinically relevant context first.

Request variant sections¶

Prediction section:

biomcp get variant "BRAF V600E" predict

ClinVar-focused section:

biomcp get variant rs113488022 clinvar

Population section:

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

CIViC section:

biomcp get variant "BRAF V600E" civic

GWAS section (trait associations from GWAS Catalog):

biomcp get variant rs7903146 gwas

All supported sections:

biomcp get variant rs113488022 all

Search variants¶

By gene and protein change:

biomcp search variant -g BRAF --hgvsp V600E --limit 5

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

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"