BGN p.Val55=
c.165C>T · VCV3685171
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.039 | GERP -3.8, phastCons 0.22 |
| Overall | ||
| CADD | 2.804 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
East Asian · 4/33,850 alleles
Filtering AF
0.00395%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00235%
Overall
0.000413%
5/1,211,710 alleles · ultra-rare
exomes 5/1,097,652 · genomes 0/114,058 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0118% | 8,463 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,653 |
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.Val55=
- Coding
- c.165C>T
- MANE Select
- NM_001711
- Type
- single nucleotide variant
- Location
- chrX:153504796 (GRCh38)
- Structure
- AlphaFold pLDDT 85.72
Similar variants
- BGN p.Val55Leu Uncertain significance ★ ⚠ same residue
- BGN c.770+1G>A Likely pathogenic ★★ same type
- BGN p.Gln75Ter Pathogenic/Likely pathogenic ★★ same type
- BGN p.Trp25Ter Likely pathogenic ★★ same type
- BGN c.909+4A>G Uncertain significance ★★ same type
- BGN p.Ala330Asp Uncertain significance ★★ ⚠ same type
- BGN p.Ala330Pro Uncertain significance ★★ ⚠ same type
- BGN p.Ala41Ser Uncertain significance ★★ ⚠ 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/bgn-p-val55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown