BNC2 p.Ser173=
c.519C>T · rs149019822 · VCV120242
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.477%, afr)
Conditions
1
hypotensive 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 4.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.477%
African / African-American · 358/75,042 alleles
Filtering AF
0.436%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.42%
Overall
0.0288%
465/1,614,174 alleles · rare
exomes 254/1,461,880 · genomes 211/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.477% | 210 |
| Middle Eastern | 0.0825% | 1,212 |
| Admixed American | 0.0783% | 1,277 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| European (non-Finnish) | 0.00297% | 33,715 |
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
- BNC2
- Protein
- p.Ser173=
- Coding
- c.519C>T
- MANE Select
- NM_017637
- dbSNP
- rs149019822
- Type
- single nucleotide variant
- Location
- chr9:16552680 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
Similar variants
- BNC2 p.Ala28= Benign ★★ same condition
- BNC2 p.Ala923Val Benign/Likely benign ★★ same condition
- BNC2 p.Asp930Gly Likely benign ★★ same condition
- BNC2 p.Ile974Val Benign ★★ same condition
- BNC2 p.Leu414Val Benign ★★ same condition
- BNC2 p.Leu826= Benign/Likely benign ★★ same condition
- BNC2 p.Phe312= Benign ★★ same condition
- BNC2 p.Pro623His Benign/Likely benign ★★ 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/bnc2-p-ser173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown