CCDC15 p.His545=
c.1635T>C · rs61912661 · VCV2642510
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.606%, nfe)
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 -0.7 | GERP 1 |
| Overall | ||
| CADD | 0.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.606%
European (non-Finnish) · 7,151/1,179,882 alleles
Filtering AF
0.594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.589%
Overall
0.495%
7,988/1,614,020 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.606% | 165 |
| Remaining individualsnot grpmax-eligible | 0.394% | 254 |
| Admixed American | 0.337% | 297 |
| Ashkenazi Jewishnot grpmax-eligible | 0.297% | 336 |
| Finnishnot grpmax-eligible | 0.272% | 368 |
| Middle Eastern | 0.264% | 379 |
| African / African-American | 0.0826% | 1,211 |
| South Asian | 0.0538% | 1,859 |
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.His545=
- Coding
- c.1635T>C
- MANE Select
- NM_025004
- dbSNP
- rs61912661
- Type
- single nucleotide variant
- Location
- chr11:124987861 (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.Pro10= Benign ★★ 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
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-his545 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown