BCR p.Pro1228=
c.3684T>C · rs55715766 · VCV733455
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.087%, 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 0.52 | GERP -0.82, phastCons 0.99 |
| Overall | ||
| CADD | 10.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.087%
East Asian · 39/44,824 alleles
Filtering AF
0.0653%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0578%
Overall
0.0469%
756/1,611,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.087% | 1,149 |
| African / African-American | 0.0562% | 1,779 |
| European (non-Finnish) | 0.0508% | 1,969 |
| Admixed American | 0.0484% | 2,068 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,466 |
| Remaining individualsnot grpmax-eligible | 0.0353% | 2,832 |
| Middle Eastern | 0.0226% | 4,430 |
| South Asian | 0.011% | 9,092 |
| Finnishnot grpmax-eligible | 0.00313% | 31,924 |
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
- BCR
- Protein
- p.Pro1228=
- Coding
- c.3684T>C
- MANE Select
- NM_004327
- dbSNP
- rs55715766
- Type
- single nucleotide variant
- Location
- chr22:23314672 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.61 · 5 PDB
- Residue 1228
- the rho-gap domain
Similar variants
- BCR p.Ser356Arg Uncertain significance ★★ ⚠ same type
- BCR c.2116-6C>G Benign/Likely benign ★★ same type
- BCR c.2116-7C>A Benign/Likely benign ★★ same type
- BCR c.2526+7G>T Benign/Likely benign ★★ same type
- BCR c.3073-8T>C Benign ★★ same type
- BCR c.3183-4G>A Benign ★★ same type
- BCR p.Ala1257= Benign/Likely benign ★★ same type
- BCR p.Ala152Val 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/bcr-p-pro1228 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown