BCR p.Phe54=
c.162C>T · rs112539379 · VCV719837
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.82%, afr)
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 2.7 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.82%
African / African-American · 1,975/70,084 alleles
Filtering AF
2.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.67%
Overall
0.15%
2,254/1,498,616 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.82% | 35 |
| Admixed American | 0.267% | 374 |
| Remaining individualsnot grpmax-eligible | 0.161% | 621 |
| Middle Eastern | 0.16% | 625 |
| European (non-Finnish) | 0.00421% | 23,745 |
| East Asian | 0.00266% | 37,650 |
| South Asian | 0.00251% | 39,895 |
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.Phe54=
- Coding
- c.162C>T
- MANE Select
- NM_004327
- dbSNP
- rs112539379
- Type
- single nucleotide variant
- Location
- chr22:23181122 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.61 · 5 PDB
- Residue 54
- the 'kinase' region; an α-helix
Similar variants
- BCR p.Phe54Ser Uncertain significance ★ ⚠ same residue
- 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
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-phe54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown