BRD9 p.Pro272=
c.816G>A · rs74984870 · VCV708816
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.46%, afr)
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 -1.8 | GERP -3.4 |
| Overall | ||
| CADD | 8.626 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.46%
African / African-American · 2,600/75,038 alleles
Filtering AF
3.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.31%
Overall
0.216%
3,491/1,613,926 alleles · low-frequency
exomes 1,932/1,461,598 · genomes 1,559/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.46% | 29 |
| Middle Eastern | 1.11% | 90 |
| Remaining individualsnot grpmax-eligible | 0.282% | 355 |
| Admixed American | 0.275% | 364 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0777% | 1,287 |
| South Asian | 0.0406% | 2,460 |
| European (non-Finnish) | 0.0358% | 2,796 |
| East Asian | 0.00223% | 44,884 |
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
- BRD9
- Protein
- p.Pro272=
- Coding
- c.816G>A
- MANE Select
- NM_023924
- dbSNP
- rs74984870
- Type
- single nucleotide variant
- Location
- chr5:886609 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.72 · 57 PDB
Similar variants
- BRD9 p.Pro272Leu Uncertain significance ★ ⚠ same residue
- BRD9 c.1526-6A>G Benign ★★ same type
- BRD9 p.Ala10Asp Uncertain significance ★ ⚠ same type
- BRD9 p.Ala20Gly Uncertain significance ★ ⚠ same type
- BRD9 p.Ala232Thr Uncertain significance ★ ⚠ same type
- BRD9 p.Ala306Thr Uncertain significance ★ ⚠ same type
- BRD9 p.Ala346Thr Uncertain significance ★ ⚠ same type
- BRD9 p.Ala537Val 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/brd9-p-pro272 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown