CCND2 c.720+195del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 55.1%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +195 | deep intronic (+195 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.041 | GERP -3.4 |
| Non-coding constraint | Z 3.62 | 1 kb window · o/e 0.71 · regional · uncalibrated |
| Overall | ||
| CADD | 1.461 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
55.1%
East Asian · 3,261/5,914 alleles
Filtering AF
53.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 52.9%
Overall
25.8%
39,318/152,216 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 55.1% | 2 |
| Admixed American | 37.8% | 3 |
| Finnishnot grpmax-eligible | 35.5% | 3 |
| Remaining individualsnot grpmax-eligible | 29.3% | 3 |
| European (non-Finnish) | 25.9% | 4 |
| South Asian | 24% | 4 |
| Middle Eastern | 21.6% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 20.1% | 5 |
| African / African-American | 15% | 7 |
| Amishnot grpmax-eligible | 11.4% | 9 |
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.720+195del
- MANE Select
- NM_001759
- dbSNP
- rs3217854
- Type
- Deletion
- Location
- chr12:4289184 (GRCh38)
- Gene constraint
- LOEUF 0.385 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.98 · 1 PDB
Similar variants
- CCND2 c.196-205_250del Uncertain significance ★ same type
- CCND2 p.Ter290= 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/ccnd2-c-720-plus-195del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown