CEP78 p.Phe16del
c.44TCT[1] · rs765143446 · VCV1105283
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 19.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
Admixed American · 85/57,680 alleles
Filtering AF
0.122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.113%
Overall
0.0212%
338/1,593,102 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.147% | 679 |
| Middle Eastern | 0.0496% | 2,015 |
| South Asian | 0.0362% | 2,760 |
| European (non-Finnish) | 0.0169% | 5,916 |
| Remaining individualsnot grpmax-eligible | 0.013% | 7,716 |
| African / African-American | 0.00938% | 10,660 |
| East Asian | 0.00684% | 14,621 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00343% | 29,194 |
| Finnishnot grpmax-eligible | 0.00168% | 59,398 |
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.Phe16del
- Coding
- c.44TCT[1]
- MANE Select
- NM_001330691
- dbSNP
- rs765143446
- Type
- Microsatellite
- Location
- chr9:78236392 (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 p.Leu286fs Pathogenic/Likely pathogenic ★★ same type
- CEP78 p.Ser696del Uncertain significance ★★ same type
- CEP78 p.Asp136fs Likely pathogenic ★ same type
- CEP78 p.Glu134fs Likely pathogenic ★ same type
- CEP78 p.Glu473_Arg474insTer Pathogenic ★ same type
- CEP78 p.Leu252fs Pathogenic ★ same type
- CEP78 p.Glu687del Uncertain significance ★ same type
- CEP78 c.1459-9_1459-7del Likely benign ★ 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-phe16del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown