CEP152 c.1908+19del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0364%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -11 |
| Non-coding constraint | Z 0.52 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 0.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0364%
Admixed American · 18/49,518 alleles
Filtering AF
0.0234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0193%
Overall
0.00238%
34/1,430,396 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0364% | 2,751 |
| Remaining individualsnot grpmax-eligible | 0.0036% | 27,816 |
| East Asian | 0.00249% | 40,210 |
| African / African-American | 0.00143% | 69,830 |
| European (non-Finnish) | 0.00115% | 87,047 |
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
- Coding
- c.1908+19del
- MANE Select
- NM_001194998
- dbSNP
- rs773691592
- Type
- Deletion
- Location
- chr15:48768937 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 p.Gln1058fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Leu1071fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Lys764fs Likely pathogenic ★★ same type
- CEP152 p.Phe225_Leu226insTer Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Thr1006fs Pathogenic/Likely pathogenic ★★ same type
- CEP152 p.Thr386fs Pathogenic ★★ same type
- CEP152 p.Tyr678_Gln679delinsTer Pathogenic ★★ same type
- CEP152 p.Val1084fs 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-c-1908-plus-19del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown