CYP2E1 p.Ser98=
c.294G>A · rs28371740 · VCV739459
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.977%, 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 -12 | GERP -3.9 |
| Overall | ||
| CADD | 0.317 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.977%
African / African-American · 733/75,044 alleles
Filtering AF
0.918%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.895%
Overall
0.0547%
882/1,613,452 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.977% | 102 |
| Admixed American | 0.0866% | 1,154 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Middle Eastern | 0.0496% | 2,015 |
| European (non-Finnish) | 0.00331% | 30,256 |
| South Asian | 0.0022% | 45,538 |
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
- CYP2E1
- Protein
- p.Ser98=
- Coding
- c.294G>A
- MANE Select
- NM_000773
- dbSNP
- rs28371740
- Type
- single nucleotide variant
- Location
- chr10:133528597 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.22 · 6 PDB
Similar variants
- CYP2E1 p.Asn204= Benign ★★ same type
- CYP2E1 p.His457Leu Benign ★★ ⚠ same type
- CYP2E1 p.Ile321= Benign ★★ same type
- CYP2E1 p.Phe421= Benign ★★ same type
- CYP2E1 p.Pro348= Benign ★★ same type
- CYP2E1 p.Ala105Val Uncertain significance ★ ⚠ same type
- CYP2E1 p.Ala175Val Uncertain significance ★ ⚠ same type
- CYP2E1 p.Ala294Ser 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/cyp2e1-p-ser98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown