CCNB2 p.Ile296=
c.888C>T · rs547886264 · VCV3139873
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0758%, 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 -3.4 | GERP -8.1 |
| Overall | ||
| CADD | 4.674 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0758%
South Asian · 69/91,050 alleles
Filtering AF
0.0613%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0561%
Overall
0.00508%
82/1,613,546 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0758% | 1,320 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,809 |
| Admixed American | 0.00167% | 60,016 |
| European (non-Finnish) | 0.000339% | 294,978 |
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
- CCNB2
- Protein
- p.Ile296=
- Coding
- c.888C>T
- MANE Select
- NM_004701
- dbSNP
- rs547886264
- Type
- single nucleotide variant
- Location
- chr15:59117281 (GRCh38)
- Gene constraint
- LOEUF 1.013 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.14
Similar variants
- CCNB2 p.Ile395Thr Benign ★★ same type
- CCNB2 p.Lys89= Benign ★★ same type
- CCNB2 p.Met100Thr Benign ★★ same type
- CCNB2 p.Ala112Gly Uncertain significance ★ ⚠ same type
- CCNB2 p.Ala167Thr Uncertain significance ★ ⚠ same type
- CCNB2 p.Ala46Thr Uncertain significance ★ ⚠ same type
- CCNB2 p.Arg164Cys Uncertain significance ★ ⚠ same type
- CCNB2 p.Arg164His 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/ccnb2-p-ile296 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown