BRD2 p.Ala59=
c.177C>A · rs138097363 · VCV720050
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.45%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.261 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.19, phastCons 1 |
| Overall | ||
| CADD | 11.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.45%
Middle Eastern · 88/6,062 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.309%
4,991/1,614,228 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.45% | 69 |
| South Asian | 0.946% | 106 |
| Ashkenazi Jewishnot grpmax-eligible | 0.719% | 139 |
| Remaining individualsnot grpmax-eligible | 0.395% | 253 |
| Admixed American | 0.381% | 262 |
| European (non-Finnish) | 0.273% | 367 |
| African / African-American | 0.139% | 721 |
| Finnishnot grpmax-eligible | 0.0359% | 2,785 |
| East Asian | 0.0178% | 5,611 |
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.Ala59=
- Coding
- c.177C>A
- MANE Select
- NM_005104
- dbSNP
- rs138097363
- Type
- single nucleotide variant
- Location
- chr6:32974609 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70 · 169 PDB
- Residue 59
- the 'disordered' region
Similar variants
- BRD2 p.Pro12Leu Uncertain significance ★★ ⚠ same type
- BRD2 p.Ala766Thr Benign/Likely benign ★★ same type
- BRD2 p.Gln533= 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
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-ala59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown