GeneBe

Annotate and classify one human genetic variant using GeneBe.

Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it). Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores (REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the GeneBe page to cite. Research use only; not a diagnosis.

Convert a variant written in any notation into normalized hg38 genomic coordinates.

Use when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID), without annotation. Does not classify the variant; use annotate_variant for that.

Explain step by step why each classification criterion did or did not apply to a variant.

Use after annotate_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.

Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity.

Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total_transcripts.

List a variant's predicted molecular consequences on every overlapping transcript.

Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.

Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t).

Check status: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target reference and warnings such as REF_MISMATCH may apply.