CEP97 p.Ser674=
c.2022C>T · rs75383743 · VCV775888
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, afr)
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 -4.7 | GERP -3.7 |
| Overall | ||
| CADD | 0.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
African / African-American · 907/75,036 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.0936%
1,511/1,614,098 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.21% | 83 |
| Remaining individualsnot grpmax-eligible | 0.147% | 679 |
| Admixed American | 0.142% | 706 |
| Middle Eastern | 0.132% | 758 |
| European (non-Finnish) | 0.035% | 2,857 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,801 |
| South Asian | 0.00439% | 22,767 |
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.Ser674=
- Coding
- c.2022C>T
- MANE Select
- NM_024548
- dbSNP
- rs75383743
- Type
- single nucleotide variant
- Location
- chr3:101764975 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.89
- Residue 674
- the 'ccp110-binding' region; 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-ser674 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown