Is BSG p.Val26Phe (c.76G>T) pathogenic?

BSG p.Val26Phe (c.76G>T) is classified Benign in BSG (ClinVar, No assertion criteria, 2 submitters; last evaluated 2024-02-02). AlphaMissense: likely benign (0.1494); Rare (popmax 0.9%, nfe); Associated with BSG-related disorder.

What condition is associated with BSG p.Val26Phe (c.76G>T)?

BSG p.Val26Phe (c.76G>T) is associated with BSG-related disorder (ClinVar).

How common is BSG p.Val26Phe (c.76G>T) in the general population?

BSG p.Val26Phe (c.76G>T) is rare (popmax 0.9%, nfe) (gnomAD).

What do computational predictors say about BSG p.Val26Phe (c.76G>T)?

AlphaMissense predicts likely benign (score 0.1494) — an in-silico prediction, not a clinical call.

BSG p.Val26Phe

c.76G>T · rs144824657 · VCV3042170

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1494 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.9%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

BSG-related disorder

Computational evidence

Protein change
AlphaMissense	0.1494	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	LLR -10.10	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 -0.88	GERP -3.9
Regional constraint	o/e 1.08	unconstrained · MANE · 9,939 bp · p 0.057 · regional, not allelic
Overall
CADD	13.73	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 0.9% European (non-Finnish) · 9,744/1,082,294 alleles

Filtering AF 0.885% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.879%

Overall 0.761% 10,786/1,417,762 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.9%	111
Admixed American	0.756%	132
Remaining individualsnot grpmax-eligible	0.63%	159
Finnishnot grpmax-eligible	0.597%	168
Middle Eastern	0.172%	580
African / African-American	0.142%	705
Ashkenazi Jewishnot grpmax-eligible	0.103%	968
South Asian	0.0225%	4,442
East Asian	0.00263%	37,976

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: BSG
Protein: p.Val26Phe
Coding: c.76G>T
MANE Select: NM_001728
dbSNP: rs144824657
Type: single nucleotide variant
Location: chr19:577782 (GRCh38)
Gene constraint: LOEUF 1.254 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.51 · 18 PDB
Residue 26: a UniProt-annotated variant site (in); a β-strand

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

Disease context

BSG-related disorder

Similar variants

BSG p.Arg380Cys Uncertain significance ★ ⚠ same condition
BSG c.1095-9G>A Benign same condition
BSG c.-89C>A Likely benign same condition
BSG p.Ala122= Likely benign same condition
BSG p.Ala225= Benign same condition
BSG p.Asp148= Likely benign same condition
BSG p.Asp181= Benign same condition
BSG p.Ile342= Likely benign same condition

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/bsg-p-val26phe (accessed [today's date]).

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