BSN p.Gln240=
c.720G>A · rs192482729 · VCV3040984
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.99%, eas)
Conditions
1
BSN-related disorder
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 5.8 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 7.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.99%
East Asian · 881/44,364 alleles
Filtering AF
1.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.83%
Overall
0.0555%
888/1,599,194 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.99% | 50 |
| Remaining individualsnot grpmax-eligible | 0.00969% | 10,317 |
| Admixed American | 0.00173% | 57,792 |
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
- BSN
- Protein
- p.Gln240=
- Coding
- c.720G>A
- MANE Select
- NM_003458
- dbSNP
- rs192482729
- Type
- single nucleotide variant
- Location
- chr3:49642354 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 (gnomAD)
- Residue 240
- the 'disordered' region
Disease context
BSN-related disorder
Similar variants
- BSN p.Arg1145Trp Uncertain significance ★★ ⚠ same condition
- BSN p.Leu2466Ile Uncertain significance ★★ same condition
- BSN p.Pro2732Arg Uncertain significance ★★ same condition
- BSN p.Gln1776Ter Likely pathogenic ★ same condition
- BSN p.Gln3155Ter Likely pathogenic ★ same condition
- BSN p.Gln875Ter Pathogenic ★ same condition
- BSN p.Arg1066Cys Uncertain significance ★ ⚠ same condition
- BSN p.Arg110Ter 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/bsn-p-gln240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown