BRD4 c.3282+4del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.82 | GERP -2.5, phastCons 0.91 |
| Non-coding constraint | Z 7.36 | 1 kb window · o/e 0.62 · regional · uncalibrated |
| Overall | ||
| CADD | 15.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
South Asian · 28/91,088 alleles
Filtering AF
0.0218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0188%
Overall
0.00192%
31/1,614,134 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0307% | 3,253 |
| Admixed American | 0.00167% | 60,020 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| European (non-Finnish) | 8.47e-05% | 1,180,030 |
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
- BRD4
- Coding
- c.3282+4del
- MANE Select
- NM_001379291
- dbSNP
- rs776518007
- Type
- Deletion
- Location
- chr19:15239906 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.20 · 613 PDB
Similar variants
- BRD4 p.Gln934_Gln936del Uncertain significance ★★ same type
- BRD4 p.Gln973_Gln989del Uncertain significance ★★ same type
- BRD4 p.Gln1105fs Likely pathogenic ★ same type
- BRD4 p.His77del Likely pathogenic ★ same type
- BRD4 p.Lys1181fs Pathogenic ★ same type
- BRD4 p.Met132fs Likely pathogenic ★ same type
- BRD4 p.Pro1171fs Likely pathogenic ★ same type
- BRD4 p.Pro237fs Likely pathogenic ★ 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/brd4-c-3282-plus-4del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown