CEP78 p.Ser28=
c.84G>C · rs10867166 · VCV517538
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 40%, mid) — 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -0.002 |
| Overall | ||
| CADD | 9.615 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
40%
Middle Eastern · 2,413/6,038 alleles
Filtering AF
38.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 38.2%
Overall
36.6%
585,706/1,599,716 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 40% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 38.6% | 3 |
| South Asian | 38.3% | 3 |
| European (non-Finnish) | 38.3% | 3 |
| Finnishnot grpmax-eligible | 37.3% | 3 |
| Remaining individualsnot grpmax-eligible | 36.3% | 3 |
| Amishnot grpmax-eligible | 33.1% | 3 |
| Admixed American | 32.2% | 3 |
| East Asian | 25.2% | 4 |
| African / African-American | 16.5% | 6 |
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
- CEP78
- Protein
- p.Ser28=
- Coding
- c.84G>C
- MANE Select
- NM_001330691
- dbSNP
- rs10867166
- Type
- single nucleotide variant
- Location
- chr9:78236434 (GRCh38)
- Gene constraint
- LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.28
Similar variants
- CEP78 c.1205+2T>A Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.1206-2A>C Pathogenic ★★ same type
- CEP78 c.1206-2A>G Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.1251+5G>A Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.254-1G>T Pathogenic/Likely pathogenic ★★ same type
- CEP78 c.778+1G>A Likely pathogenic ★★ same type
- CEP78 p.Arg483Ter Pathogenic/Likely pathogenic ★★ same type
- CEP78 p.Cys158Phe 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/cep78-p-ser28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown