CCNB2 p.Lys89=
c.267G>A · rs35033821 · VCV777248
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.68 | loss · gain 0.26 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 3.5, phastCons 1 |
| Overall | ||
| CADD | 22.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
European (non-Finnish) · 13,528/1,178,562 alleles
Filtering AF
1.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.903%
14,554/1,611,998 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.15% | 87 |
| Remaining individualsnot grpmax-eligible | 0.713% | 140 |
| Finnishnot grpmax-eligible | 0.343% | 292 |
| Admixed American | 0.276% | 362 |
| African / African-American | 0.171% | 586 |
| Middle Eastern | 0.0826% | 1,211 |
| South Asian | 0.0561% | 1,783 |
| Ashkenazi Jewishnot grpmax-eligible | 0.044% | 2,275 |
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.Lys89=
- Coding
- c.267G>A
- MANE Select
- NM_004701
- dbSNP
- rs35033821
- Type
- single nucleotide variant
- Location
- chr15:59107670 (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.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
- CCNB2 p.Arg196Gln 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-lys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown