CCDC15 p.Pro10=
c.30T>C · rs141534483 · VCV779149
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.18%, 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 2.2 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 7.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.18%
African / African-American · 1,638/75,016 alleles
Filtering AF
2.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.06%
Overall
0.155%
2,501/1,613,904 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.18% | 46 |
| Admixed American | 0.322% | 311 |
| Middle Eastern | 0.313% | 319 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| European (non-Finnish) | 0.0425% | 2,350 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| South Asian | 0.0022% | 45,539 |
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
- CCDC15
- Protein
- p.Pro10=
- Coding
- c.30T>C
- MANE Select
- NM_025004
- dbSNP
- rs141534483
- Type
- single nucleotide variant
- Location
- chr11:124954762 (GRCh38)
- Gene constraint
- LOEUF 1.265 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.02
Similar variants
- CCDC15 p.Arg181Cys Uncertain significance ★★ ⚠ same type
- CCDC15 p.Ala110Thr Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala140Val Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala19Thr Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala44Ser Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala44Val Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala6Thr Uncertain significance ★ ⚠ same type
- CCDC15 p.Ala815Ser 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/ccdc15-p-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown