Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.87%, eas) — 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP -1.9, phastCons 0.035 |
| Overall | ||
| CADD | 7.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.87%
East Asian · 2,810/40,918 alleles
Filtering AF
6.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.57%
Overall
0.4%
6,210/1,551,600 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 6.87% | 15 |
| African / African-American | 3.66% | 27 |
| Remaining individualsnot grpmax-eligible | 0.554% | 181 |
| Admixed American | 0.449% | 223 |
| Middle Eastern | 0.117% | 856 |
| South Asian | 0.0595% | 1,681 |
| European (non-Finnish) | 0.00881% | 11,356 |
| Finnishnot grpmax-eligible | 0.00167% | 59,884 |
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
- CEP295
- Protein
- p.Ser988=
- Coding
- c.2964C>T
- MANE Select
- NM_033395
- dbSNP
- rs3802770
- Type
- single nucleotide variant
- Location
- chr11:93697876 (GRCh38)
- Gene constraint
- LOEUF 0.735 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 44.76
- Residue 988
- a UniProt-annotated variant site (in sckl11; likely pathogenic)
Similar variants
- CEP295 p.Gln2146His Uncertain significance ★★ ⚠ same type
- CEP295 p.Gln998Arg Uncertain significance ★★ ⚠ same type
- CEP295 p.Thr451Arg Uncertain significance ★★ ⚠ same type
- CEP295 p.Gln1506= Benign ★★ same type
- CEP295 p.Gln1728= Benign ★★ same type
- CEP295 p.Gln80Lys Benign ★★ same type
- CEP295 p.Glu1026Lys Benign ★★ ⚠ same type
- CEP295 p.Glu179Lys 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/cep295-p-ser988 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown