BCR p.Ala131=
c.393C>A · rs528616365 · VCV2652957
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, nfe)
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 -2.5 | GERP -3.7 |
| Overall | ||
| CADD | 2.246 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
European (non-Finnish) · 125/1,134,630 alleles
Filtering AF
0.00942%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00878%
Overall
0.00863%
130/1,506,448 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.011% | 9,077 |
| African / African-American | 0.00424% | 23,594 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00416% | 24,032 |
| Remaining individualsnot grpmax-eligible | 0.00173% | 57,870 |
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.Ala131=
- Coding
- c.393C>A
- MANE Select
- NM_004327
- dbSNP
- rs528616365
- Type
- single nucleotide variant
- Location
- chr22:23181353 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.61 · 5 PDB
- Residue 131
- the 'kinase' region; the 'disordered' region
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-ala131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown