CEP152 p.Phe218=
c.654C>T · rs367623474 · VCV2672589
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00267%, 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 0.62 | GERP 1.4, phastCons 0.87 |
| Overall | ||
| CADD | 7.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,870 alleles
Filtering AF
0.000689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00118%
19/1,613,688 alleles · very rare
exomes 13/1,461,668 · genomes 6/152,020 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,435 |
| East Asian | 0.00223% | 44,880 |
| South Asian | 0.0022% | 45,535 |
| European (non-Finnish) | 0.00119% | 84,275 |
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
- CEP152
- Protein
- p.Phe218=
- Coding
- c.654C>T
- MANE Select
- NM_001194998
- dbSNP
- rs367623474
- Type
- single nucleotide variant
- Location
- chr15:48796047 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 p.Phe218Leu Uncertain significance ★ ⚠ same residue
- CEP152 c.1578-1G>A Likely pathogenic ★★ same type
- CEP152 c.1908+1G>T Likely pathogenic ★★ same type
- CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same type
- CEP152 c.88-2A>G Likely pathogenic ★★ same type
- CEP152 c.972+2T>A Likely pathogenic ★★ same type
- CEP152 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Arg1309Ter 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/cep152-p-phe218 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown