CCND2 c.195+269A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.977%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +269 | deep intronic (+269 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.084 | GERP -2.7, phastCons 0.006 |
| Non-coding constraint | Z 7.71 | 1 kb window · o/e 0.61 · regional · uncalibrated |
| Overall | ||
| CADD | 0.329 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.977%
African / African-American · 406/41,562 alleles
Filtering AF
0.898%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.868%
Overall
0.286%
435/152,292 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.977% | 102 |
| Remaining individualsnot grpmax-eligible | 0.189% | 528 |
| Admixed American | 0.163% | 612 |
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
- CCND2
- Coding
- c.195+269A>C
- MANE Select
- NM_001759
- dbSNP
- rs114215980
- Type
- single nucleotide variant
- Location
- chr12:4274504 (GRCh38)
- Gene constraint
- LOEUF 0.385 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.98 · 1 PDB
Similar variants
- CCND2 p.Gln277Ter Pathogenic/Likely pathogenic ★★ same type
- CCND2 p.Pro281Ala Pathogenic ★★ same type
- CCND2 p.Pro281Ser Pathogenic/Likely pathogenic ★★ same type
- CCND2 p.Ser271Ter Likely pathogenic ★★ same type
- CCND2 p.Thr280Ala Pathogenic ★★ same type
- CCND2 p.Thr280Asn Pathogenic/Likely pathogenic ★★ same type
- CCND2 p.Thr280Ile Pathogenic/Likely pathogenic ★★ same type
- CCND2 p.Thr280Pro Pathogenic/Likely pathogenic ★★ ⚠ 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/ccnd2-c-195-plus-269a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown