CCNB3 p.Ala702=
c.2106C>T · rs73213610 · VCV709387
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.122%, sas)
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 -0.8 | GERP -2.8 |
| Overall | ||
| CADD | 0.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.122%
South Asian · 69/56,671 alleles
Filtering AF
0.0987%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0903%
Overall
0.0594%
719/1,209,518 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.122% | 821 |
| European (non-Finnish) | 0.0694% | 1,441 |
| Remaining individualsnot grpmax-eligible | 0.0357% | 2,799 |
| Middle Eastern | 0.023% | 4,346 |
| Admixed American | 0.0109% | 9,156 |
| African / African-American | 0.00697% | 14,350 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00454% | 22,030 |
| East Asian | 0.00297% | 33,699 |
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.Ala702=
- Coding
- c.2106C>T
- MANE Select
- NM_033031
- dbSNP
- rs73213610
- Type
- single nucleotide variant
- Location
- chrX:50310275 (GRCh38)
- Structure
- AlphaFold pLDDT 42.25
Similar variants
- CCNB3 p.Ala702Thr Likely benign ★ same residue
- 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-ala702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown