BSN p.Ala3904=
c.11712A>G · rs41290710 · VCV787167
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.914%, sas)
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 -0.33 | GERP -0.79, phastCons 0.001 |
| Overall | ||
| CADD | 5.782 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.914%
South Asian · 828/90,600 alleles
Filtering AF
0.862%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.842%
Overall
0.707%
11,377/1,609,776 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.914% | 109 |
| European (non-Finnish) | 0.81% | 124 |
| Remaining individualsnot grpmax-eligible | 0.605% | 165 |
| Middle Eastern | 0.464% | 216 |
| Amishnot grpmax-eligible | 0.44% | 228 |
| Admixed American | 0.376% | 266 |
| Ashkenazi Jewishnot grpmax-eligible | 0.318% | 315 |
| Finnishnot grpmax-eligible | 0.311% | 321 |
| African / African-American | 0.116% | 861 |
| East Asian | 0.00446% | 22,416 |
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.Ala3904=
- Coding
- c.11712A>G
- MANE Select
- NM_003458
- dbSNP
- rs41290710
- Type
- single nucleotide variant
- Location
- chr3:49664526 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 (gnomAD)
Similar variants
- BSN p.Ala1623Thr Uncertain significance ★★ ⚠ same type
- BSN p.Ala2329Val Uncertain significance ★★ ⚠ same type
- BSN p.Ala2475Pro Uncertain significance ★★ ⚠ same type
- BSN p.Arg1145Trp Uncertain significance ★★ ⚠ same type
- BSN p.Arg2221His Uncertain significance ★★ ⚠ same type
- BSN p.Arg3229Gln Uncertain significance ★★ same type
- BSN p.Arg976His Uncertain significance ★★ same type
- BSN p.His1842Arg 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/bsn-p-ala3904 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown