CCNB3 p.Ala792=
c.2376G>A · rs374751350 · VCV2660546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 1.063 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
European (non-Finnish) · 151/895,028 alleles
Filtering AF
0.0147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.0137%
166/1,209,947 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0169% | 5,927 |
| African / African-American | 0.0122% | 8,196 |
| Remaining individualsnot grpmax-eligible | 0.0084% | 11,898 |
| East Asian | 0.00592% | 16,880 |
| Admixed American | 0.00218% | 45,775 |
| South Asian | 0.00176% | 56,680 |
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
- CCNB3
- Protein
- p.Ala792=
- Coding
- c.2376G>A
- MANE Select
- NM_033031
- dbSNP
- rs374751350
- Type
- single nucleotide variant
- Location
- chrX:50310545 (GRCh38)
- Structure
- AlphaFold pLDDT 42.25
Similar variants
- CCNB3 p.Ala702= Benign ★★ same type
- CCNB3 p.Gly1001Arg Benign ★★ same type
- CCNB3 p.Lys857Gln Likely benign ★★ ⚠ same type
- CCNB3 p.Ser188Thr Benign ★★ ⚠ same type
- CCNB3 p.Ala1208Thr Uncertain significance ★ ⚠ same type
- CCNB3 p.Ala312Pro Uncertain significance ★ ⚠ same type
- CCNB3 p.Ala437Ser Uncertain significance ★ ⚠ same type
- CCNB3 p.Ala981Thr 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/ccnb3-p-ala792 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown