Is BGN p.Ile188= (c.564C>T) pathogenic?

BGN p.Ile188= (c.564C>T) is classified Benign/Likely benign in BGN (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Common (popmax 8.17%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Cardiovascular phenotype.

What condition is associated with BGN p.Ile188= (c.564C>T)?

BGN p.Ile188= (c.564C>T) is associated with Cardiovascular phenotype (ClinVar).

BGN p.Ile188=

Q: How common is BGN p.Ile188= (c.564C>T) in the general population?

BGN p.Ile188= (c.564C>T) is common (popmax 8.17%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.564C>T · rs2070933 · VCV1167739

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Common

common (popmax 8.17%, afr) — too common for a highly-penetrant pathogenic allele

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 -5.2	GERP -3.1
Overall
CADD	0.217	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.17% African / African-American · 4,674/57,225 alleles

Filtering AF 7.97% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.89%

Overall 1.72% 20,757/1,207,610 alleles · common exomes 16,939/1,095,322 · genomes 3,818/112,288 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	8.17%	12
East Asian	7.59%	13
Ashkenazi Jewishnot grpmax-eligible	5.55%	18
Remaining individualsnot grpmax-eligible	2.19%	46
Middle Eastern	1.7%	59
European (non-Finnish)	1.11%	90
Admixed American	1.01%	99
South Asian	0.894%	112
Finnishnot grpmax-eligible	0.732%	137

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.Ile188=
Coding: c.564C>T
MANE Select: NM_001711
dbSNP: rs2070933
Type: single nucleotide variant
Location: chrX:153506075 (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 p.Ile188Met Uncertain significance ★ same residue
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

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-ile188 (accessed [today's date]).

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