Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.34%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 0.57, phastCons 1 |
| Overall | ||
| CADD | 10.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.34%
East Asian · 602/44,824 alleles
Filtering AF
1.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
0.0496%
800/1,612,478 alleles · low-frequency
exomes 716/1,460,172 · genomes 84/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.34% | 74 |
| Finnishnot grpmax-eligible | 0.0937% | 1,067 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| Admixed American | 0.045% | 2,222 |
| South Asian | 0.0362% | 2,760 |
| European (non-Finnish) | 0.00382% | 26,190 |
| African / African-American | 0.00133% | 75,022 |
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.Leu19=
- Coding
- c.55T>C
- MANE Select
- NM_005104
- dbSNP
- rs3752528
- Type
- single nucleotide variant
- Location
- chr6:32974487 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.70 · 169 PDB
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-leu19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown