CCNA1 p.Ser145=
c.435A>G · rs1317006880 · VCV752033
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.40 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 1.263 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,938 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000372%
6/1,613,280 alleles · very rare
exomes 5/1,461,094 · genomes 1/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,969 |
| African / African-American | 0.00133% | 74,912 |
| European (non-Finnish) | 0.000254% | 393,167 |
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
- CCNA1
- Protein
- p.Ser145=
- Coding
- c.435A>G
- MANE Select
- NM_001413923
- dbSNP
- rs1317006880
- Type
- single nucleotide variant
- Location
- chr13:36438089 (GRCh38)
- Gene constraint
- LOEUF 0.583 · pLI 0.46 (gnomAD)
- Structure
- AlphaFold pLDDT 68.65
Similar variants
- CCNA1 c.412+5C>A Benign ★★ same type
- CCNA1 p.Leu342= Benign ★★ same type
- CCNA1 p.Thr196= Benign ★★ same type
- CCNA1 p.Tyr63= Benign ★★ same type
- CCNA1 c.-101C>G Uncertain significance ★ ⚠ same type
- CCNA1 c.-19G>C Uncertain significance ★ ⚠ same type
- CCNA1 c.-50C>T Uncertain significance ★ ⚠ same type
- CCNA1 c.-51C>A 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/ccna1-p-ser145 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown