CEP104 c.1317+252A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.23%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +252 | deep intronic (+252 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.66 | GERP 0.028, phastCons 0.006 |
| Overall | ||
| CADD | 4.463 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.23%
African / African-American · 1,324/40,932 alleles
Filtering AF
3.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.03%
Overall
0.932%
1,404/150,628 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.23% | 31 |
| Remaining individualsnot grpmax-eligible | 0.718% | 139 |
| Admixed American | 0.397% | 252 |
| European (non-Finnish) | 0.00736% | 13,583 |
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
- CEP104
- Coding
- c.1317+252A>C
- MANE Select
- NM_014704
- dbSNP
- rs7540242
- Type
- single nucleotide variant
- Location
- chr1:3836243 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.75 · 2 PDB
Similar variants
- CEP104 c.2364+1G>A Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg299Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg55Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Arg631Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Glu627Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Lys270Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 p.Tyr253Ter Pathogenic/Likely pathogenic ★★ same type
- CEP104 c.1120-5T>A 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/cep104-c-1317-plus-252a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown