CD82 p.Gly233=
c.699C>T · rs79095986 · VCV786594
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.97%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.34 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.069 | GERP 0.16, phastCons 0.89 |
| Overall | ||
| CADD | 9.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.97%
African / African-American · 2,979/74,982 alleles
Filtering AF
3.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.81%
Overall
0.22%
3,545/1,613,228 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.97% | 25 |
| Admixed American | 0.378% | 264 |
| Remaining individualsnot grpmax-eligible | 0.283% | 353 |
| Middle Eastern | 0.182% | 551 |
| East Asian | 0.0335% | 2,987 |
| South Asian | 0.0187% | 5,357 |
| European (non-Finnish) | 0.01% | 9,998 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
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
- CD82
- Protein
- p.Gly233=
- Coding
- c.699C>T
- MANE Select
- NM_002231
- dbSNP
- rs79095986
- Type
- single nucleotide variant
- Location
- chr11:44618696 (GRCh38)
- Gene constraint
- LOEUF 1.221 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.31 · 1 PDB
Similar variants
- CD82 p.Leu248= Benign ★★ same type
- CD82 p.Val62= Benign ★★ same type
- CD82 p.Ala195Val Uncertain significance ★ ⚠ same type
- CD82 p.Arg254Trp Uncertain significance ★ ⚠ same type
- CD82 p.Arg53Ser Uncertain significance ★ ⚠ same type
- CD82 p.Asn109Ser Uncertain significance ★ ⚠ same type
- CD82 p.Asn17Ser Uncertain significance ★ ⚠ same type
- CD82 p.Asn227Thr 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/cd82-p-gly233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown