BRD1 p.Arg1020=
c.3060C>T · rs114483505 · VCV781531
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.85%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.047 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 9.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.85%
African / African-American · 2,891/75,070 alleles
Filtering AF
3.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.69%
Overall
0.193%
3,119/1,613,376 alleles · low-frequency
exomes 1,497/1,460,982 · genomes 1,622/152,394 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.85% | 26 |
| Remaining individualsnot grpmax-eligible | 0.182% | 548 |
| Admixed American | 0.132% | 760 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00329% | 30,363 |
| European (non-Finnish) | 0.00246% | 40,690 |
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
- BRD1
- Protein
- p.Arg1020=
- Coding
- c.3060C>T
- MANE Select
- NM_001304808
- dbSNP
- rs114483505
- Type
- single nucleotide variant
- Location
- chr22:49777095 (GRCh38)
- Gene constraint
- LOEUF 0.337 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.54 · 318 PDB
- Residue 1020
- an α-helix
Similar variants
- BRD1 p.Arg1020His Uncertain significance ★ ⚠ same residue
- BRD1 c.1657-4C>T Likely benign ★★ same type
- BRD1 p.Ala1053= Benign ★★ same type
- BRD1 p.Ala730Thr Benign ★★ same type
- BRD1 p.Gly620= Likely benign ★★ same type
- BRD1 p.Gly776Arg Benign ★★ same type
- BRD1 p.Phe193= Benign ★★ same type
- BRD1 p.Pro111= Benign ★★ 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/brd1-p-arg1020 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown