BNC2 p.Phe312=
c.936C>T · rs77464990 · VCV120245
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.94%, afr)
Conditions
1
hypotensive disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -3.7 |
| Overall | ||
| CADD | 1.796 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.94%
African / African-American · 2,956/75,000 alleles
Filtering AF
3.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.77%
Overall
0.229%
3,694/1,614,120 alleles · low-frequency
exomes 1,978/1,461,884 · genomes 1,716/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.94% | 25 |
| Middle Eastern | 0.429% | 233 |
| Remaining individualsnot grpmax-eligible | 0.326% | 306 |
| Admixed American | 0.283% | 353 |
| Ashkenazi Jewishnot grpmax-eligible | 0.166% | 604 |
| European (non-Finnish) | 0.0231% | 4,322 |
| South Asian | 0.0132% | 7,590 |
| Finnishnot grpmax-eligible | 0.00625% | 16,008 |
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.Phe312=
- Coding
- c.936C>T
- MANE Select
- NM_017637
- dbSNP
- rs77464990
- Type
- single nucleotide variant
- Location
- chr9:16437258 (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.Pro623His Benign/Likely benign ★★ same condition
- BNC2 p.Ser173= 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-phe312 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown