Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.49%, 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 -0.89 | GERP -0.65 |
| Overall | ||
| CADD | 3.358 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.49%
African / African-American · 1,115/74,730 alleles
Filtering AF
1.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.0756%
1,214/1,605,662 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.49% | 67 |
| Admixed American | 0.0835% | 1,197 |
| Remaining individualsnot grpmax-eligible | 0.074% | 1,352 |
| South Asian | 0.00226% | 44,221 |
| European (non-Finnish) | 0.00017% | 588,280 |
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
- CYP2J2
- Protein
- p.Val499=
- Coding
- c.1497T>A
- MANE Select
- NM_000775
- dbSNP
- rs2228114
- Type
- single nucleotide variant
- Location
- chr1:59893663 (GRCh38)
- Gene constraint
- LOEUF 1.061 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.90
Similar variants
- CYP2J2 p.His103= Benign ★★ same type
- CYP2J2 p.Ala133Thr Uncertain significance ★ ⚠ same type
- CYP2J2 p.Ala14Pro Uncertain significance ★ ⚠ same type
- CYP2J2 p.Ala163Thr Uncertain significance ★ ⚠ same type
- CYP2J2 p.Ala454Ser Uncertain significance ★ ⚠ same type
- CYP2J2 p.Ala4Glu Uncertain significance ★ ⚠ same type
- CYP2J2 p.Ala9Ser Uncertain significance ★ ⚠ same type
- CYP2J2 p.Arg117Gln 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/cyp2j2-p-val499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown