CEP78 c.1069+196T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 11.3%, amr) — 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 | ||
| Splice region | donor +196 | deep intronic (+196 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.26 | GERP -2.8 |
| Non-coding constraint | Z -1.34 | 1 kb window · o/e 1.11 · regional · uncalibrated |
| Overall | ||
| CADD | 3.884 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.3%
Admixed American · 2,072/18,320 alleles
Filtering AF
10.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.7%
Overall
5.64%
14,910/264,464 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 11.3% | 9 |
| Finnishnot grpmax-eligible | 10.6% | 9 |
| African / African-American | 8.88% | 11 |
| East Asian | 8.33% | 12 |
| South Asian | 6.19% | 16 |
| Remaining individualsnot grpmax-eligible | 5.27% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 3.97% | 25 |
| Middle Eastern | 3.09% | 32 |
| European (non-Finnish) | 3.03% | 33 |
| Amishnot grpmax-eligible | 0.329% | 304 |
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
- Coding
- c.1069+196T>C
- MANE Select
- NM_001330691
- dbSNP
- rs11137574
- Type
- single nucleotide variant
- Location
- chr9:78249069 (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-c-1069-plus-196t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown