BSN p.His3535=
c.10605C>T · rs1002615689 · VCV748440
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 1.5 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 6.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,008 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000372%
6/1,613,614 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,004 |
| East Asian | 0.00223% | 44,892 |
| European (non-Finnish) | 0.000254% | 393,349 |
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.His3535=
- Coding
- c.10605C>T
- MANE Select
- NM_003458
- dbSNP
- rs1002615689
- Type
- single nucleotide variant
- Location
- chr3:49662450 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 (gnomAD)
- Residue 3535
- the 'disordered' region
Similar variants
- BSN p.His3535Tyr Uncertain significance ★ same residue
- 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
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-his3535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown