Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.04%, afr)
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 -0.036 | phastCons 0.68 |
| Overall | ||
| CADD | 6.447 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.04%
African / African-American · 2,277/74,970 alleles
Filtering AF
2.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.89%
Overall
0.159%
2,565/1,614,042 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.04% | 33 |
| Remaining individualsnot grpmax-eligible | 0.139% | 718 |
| Admixed American | 0.137% | 732 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.00878% | 11,385 |
| European (non-Finnish) | 0.00873% | 11,456 |
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
- CCNG2
- Protein
- p.Leu280=
- Coding
- c.840C>T
- MANE Select
- NM_004354
- dbSNP
- rs4150086
- Type
- single nucleotide variant
- Location
- chr4:77164408 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 80.23
Similar variants
- CCNG2 p.Leu17= Benign ★★ same type
- CCNG2 p.Ser136= Benign ★★ same type
- CCNG2 p.Ala207Ser Uncertain significance ★ ⚠ same type
- CCNG2 p.Arg111Gly Uncertain significance ★ ⚠ same type
- CCNG2 p.Arg111Ile Uncertain significance ★ ⚠ same type
- CCNG2 p.Arg127Gln Uncertain significance ★ ⚠ same type
- CCNG2 p.Arg275His Uncertain significance ★ ⚠ same type
- CCNG2 p.Arg86Thr 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/ccng2-p-leu280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown