Is BEAN1 p.Arg69Trp (c.205C>T) pathogenic?

BEAN1 p.Arg69Trp (c.205C>T) is classified Likely benign in BEAN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-16). AlphaMissense: likely benign (0.166); Rare (popmax 0.897%, eas).

How common is BEAN1 p.Arg69Trp (c.205C>T) in the general population?

BEAN1 p.Arg69Trp (c.205C>T) is rare (popmax 0.897%, eas) (gnomAD).

What do computational predictors say about BEAN1 p.Arg69Trp (c.205C>T)?

AlphaMissense predicts likely benign (score 0.166) — an in-silico prediction, not a clinical call.

BEAN1 p.Arg69Trp

c.205C>T · VCV4930375

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.166 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.897%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.166	likely benign
REVEL	0.083	moderately benign-leaning
SaProt	LLR -10.48	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 0.21, phastCons 0.99
Regional constraint	o/e 0.96	unconstrained · MANE · 43 kb · p 0.44 · regional, not allelic
Overall
CADD	23.2	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 0.897% East Asian · 367/40,900 alleles

Filtering AF 0.822% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.792%

Overall 0.0291% 447/1,535,966 alleles · rare exomes 387/1,383,800 · genomes 60/152,166 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.897%	111
Remaining individualsnot grpmax-eligible	0.055%	1,818
South Asian	0.0286%	3,502
Admixed American	0.00392%	25,503
Finnishnot grpmax-eligible	0.00225%	44,492
European (non-Finnish)	0.00174%	57,344

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: BEAN1
Protein: p.Arg69Trp
Coding: c.205C>T
MANE Select: NM_001178020
Type: single nucleotide variant
Location: chr16:66469781 (GRCh38)
Gene constraint: LOEUF 1.45 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.44

Full BEAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BEAN1 p.Arg69Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
BEAN1 p.Ala156Ser Uncertain significance ★★ ⚠ same type
BEAN1 p.Arg90Gln Uncertain significance ★★ ⚠ same type
BEAN1 p.Arg108His Likely benign ★★ same type
BEAN1 p.Arg76Ser Benign/Likely benign ★★ same type
BEAN1 p.Pro167= Likely benign ★★ same type
BEAN1 p.Tyr216= Likely benign ★★ same type
BEAN1 p.Tyr96= Likely benign ★★ same type

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/bean1-p-arg69trp (accessed [today's date]).

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