BNC2 p.Ala802=
c.2406C>T · VCV4691467
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, eas)
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 -0.67 | GERP -3.4 |
| Overall | ||
| CADD | 3.551 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,864 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.00198%
32/1,613,996 alleles · ultra-rare
exomes 25/1,461,884 · genomes 7/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,205 |
| Middle Eastern | 0.0165% | 6,060 |
| African / African-American | 0.004% | 24,991 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| Admixed American | 0.00167% | 60,000 |
| European (non-Finnish) | 0.00102% | 98,333 |
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.Ala802=
- Coding
- c.2406C>T
- MANE Select
- NM_017637
- Type
- single nucleotide variant
- Location
- chr9:16435788 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
Similar variants
- BNC2 p.Ala386Val Uncertain significance ★★ ⚠ same type
- BNC2 p.Arg536Gln Uncertain significance ★★ ⚠ same type
- BNC2 p.Arg875His Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn1032Ser Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn1088Asp Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn668Ser Uncertain significance ★★ ⚠ same type
- BNC2 p.Asn795Ser Uncertain significance ★★ ⚠ same type
- BNC2 p.Asp690Glu 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/bnc2-p-ala802 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown