BCR p.Ile456=
c.1368T>C · rs55938746 · VCV732834
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0908%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.2 | GERP -3.1 |
| Overall | ||
| CADD | 6.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0908%
European (non-Finnish) · 1,071/1,179,978 alleles
Filtering AF
0.0862%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0844%
Overall
0.0715%
1,153/1,613,186 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0908% | 1,102 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,602 |
| Finnishnot grpmax-eligible | 0.0411% | 2,431 |
| Admixed American | 0.0133% | 7,502 |
| African / African-American | 0.012% | 8,332 |
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.Ile456=
- Coding
- c.1368T>C
- MANE Select
- NM_004327
- dbSNP
- rs55938746
- Type
- single nucleotide variant
- Location
- chr22:23253887 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.61 · 5 PDB
- Residue 456
- the 'disordered' region
Similar variants
- BCR p.Ile456Thr 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-ile456 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown