Is BCAN p.Ala899Thr (c.2695G>A) pathogenic?

BCAN p.Ala899Thr (c.2695G>A) is classified Likely benign in BCAN (ClinVar, Single submitter, 1 submitter; last evaluated 2018-08-09). AlphaMissense: likely benign (0.0789); Rare (popmax 0.464%, eas).

How common is BCAN p.Ala899Thr (c.2695G>A) in the general population?

BCAN p.Ala899Thr (c.2695G>A) is rare (popmax 0.464%, eas) (gnomAD).

What do computational predictors say about BCAN p.Ala899Thr (c.2695G>A)?

AlphaMissense predicts likely benign (score 0.0789) — an in-silico prediction, not a clinical call.

BCAN p.Ala899Thr

c.2695G>A · rs202001625 · VCV721309

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0789 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.464%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0789	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -6.57	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.67	GERP 0.7, phastCons 0.088
Regional constraint	o/e 0.95	unconstrained · MANE · 11 kb · p 0.11 · regional, not allelic
Overall
CADD	16.17	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.464% East Asian · 205/44,214 alleles

Filtering AF 0.412% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.392%

Overall 0.015% 240/1,595,028 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.464%	216
South Asian	0.016%	6,239
Remaining individualsnot grpmax-eligible	0.00646%	15,478
European (non-Finnish)	0.00145%	68,967

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BCAN
Protein: p.Ala899Thr
Coding: c.2695G>A
dbSNP: rs202001625
Type: single nucleotide variant
Location: chr1:156659093 (GRCh38)

Full BCAN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcan-p-ala899thr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown