Is BGN p.Pro297= (c.891A>G) pathogenic?

BGN p.Pro297= (c.891A>G) is classified Likely benign in BGN (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-05). Very rare (popmax 0.0055%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with BGN p.Pro297= (c.891A>G)?

BGN p.Pro297= (c.891A>G) is associated with Cardiovascular phenotype (ClinVar).

How common is BGN p.Pro297= (c.891A>G) in the general population?

BGN p.Pro297= (c.891A>G) is very rare (popmax 0.0055%, nfe) (gnomAD).

BGN p.Pro297=

c.891A>G · rs782750179 · VCV1550272

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0055%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.1	GERP -4.1
Overall
CADD	0.152	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0055% European (non-Finnish) · 49/890,882 alleles

Filtering AF 0.00421% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00379%

Overall 0.00457% 55/1,202,220 alleles · very rare exomes 51/1,089,526 · genomes 4/112,694 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0055%	18,181
South Asian	0.00541%	18,483
Remaining individualsnot grpmax-eligible	0.00423%	23,615
Admixed American	0.00221%	45,202

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: BGN
Protein: p.Pro297=
Coding: c.891A>G
MANE Select: NM_001711
dbSNP: rs782750179
Type: single nucleotide variant
Location: chrX:153507167 (GRCh38)
Structure: AlphaFold pLDDT 85.72

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BGN c.909+4A>G Uncertain significance ★★ same condition
BGN p.Ala330Asp Uncertain significance ★★ ⚠ same condition
BGN p.Ala330Pro Uncertain significance ★★ ⚠ same condition
BGN p.Ala41Ser Uncertain significance ★★ ⚠ same condition
BGN p.Ala44Thr Uncertain significance ★★ ⚠ same condition
BGN p.Arg106His Uncertain significance ★★ ⚠ same condition
BGN p.Arg170Cys Uncertain significance ★★ ⚠ same condition
BGN p.Arg170His Uncertain significance ★★ ⚠ 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/bgn-p-pro297 (accessed [today's date]).

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