BRD2 p.Gln533=
c.1599A>G · rs191317139 · VCV776593
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0852%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.397 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.63 | GERP -3.7 |
| Overall | ||
| CADD | 4.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0852%
Admixed American · 51/59,830 alleles
Filtering AF
0.0665%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.00459%
74/1,612,412 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0852% | 1,173 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,817 |
| European (non-Finnish) | 0.00161% | 62,099 |
| African / African-American | 0.00134% | 74,850 |
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
- BRD2
- Protein
- p.Gln533=
- Coding
- c.1599A>G
- MANE Select
- NM_005104
- dbSNP
- rs191317139
- Type
- single nucleotide variant
- Location
- chr6:32978146 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70 · 169 PDB
- Residue 533
- the 'disordered' region
Similar variants
- BRD2 p.Pro12Leu Uncertain significance ★★ ⚠ same type
- BRD2 p.Ala766Thr Benign/Likely benign ★★ same type
- BRD2 p.Leu383= Likely benign ★★ same type
- BRD2 p.Ser397= Benign/Likely benign ★★ same type
- BRD2 p.Val465= Likely benign ★★ same type
- BRD2 p.Ala263Val Uncertain significance ★ ⚠ same type
- BRD2 p.Ala295Pro Uncertain significance ★ ⚠ same type
- BRD2 p.Ala295Ser 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/brd2-p-gln533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown