CEP97 p.Gln846=
c.2538G>A · rs2625282 · VCV1625089
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 99.1%, 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 1.9 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 3.483 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
99.1%
East Asian · 44,482/44,872 alleles
Filtering AF
98.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98%
Overall
90.9%
1,466,553/1,614,070 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 99.1% | 1 |
| Admixed American | 93.7% | 1 |
| Amishnot grpmax-eligible | 93.5% | 1 |
| Finnishnot grpmax-eligible | 92.7% | 1 |
| European (non-Finnish) | 91.2% | 1 |
| Remaining individualsnot grpmax-eligible | 90.2% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 89.7% | 1 |
| African / African-American | 86.6% | 1 |
| Middle Eastern | 84.7% | 1 |
| South Asian | 84.5% | 1 |
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
- CEP97
- Protein
- p.Gln846=
- Coding
- c.2538G>A
- MANE Select
- NM_024548
- dbSNP
- rs2625282
- Type
- single nucleotide variant
- Location
- chr3:101765491 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.89
- Residue 846
- the 'interaction with mphosph9' region
Similar variants
- CEP97 p.Ala164Thr Uncertain significance ★★ ⚠ same type
- CEP97 p.Ala624Gly Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg259Gln Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg468Ile Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg570Gln Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg585Cys Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg591Cys Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg615Cys 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/cep97-p-gln846 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown