BRD1 p.Ile124=
c.372C>T · rs762464745 · VCV2653350
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -5.2 |
| Overall | ||
| CADD | 0.431 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,902 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00297%
48/1,614,030 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,980 |
| African / African-American | 0.004% | 24,980 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.00314% | 31,893 |
| Finnishnot grpmax-eligible | 0.00313% | 31,977 |
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.Ile124=
- Coding
- c.372C>T
- MANE Select
- NM_001304808
- dbSNP
- rs762464745
- Type
- single nucleotide variant
- Location
- chr22:49823946 (GRCh38)
- Gene constraint
- LOEUF 0.337 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.54 · 318 PDB
Similar variants
- BRD1 c.1657-4C>T Likely benign ★★ same type
- BRD1 p.Ala1053= Benign ★★ same type
- BRD1 p.Ala730Thr Benign ★★ same type
- BRD1 p.Arg1020= 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-ile124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown