BCR p.Ser1030=
c.3090G>A · rs766103643 · VCV780198
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0263%, 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 -10 | GERP -3.4 |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0263%
East Asian · 11/41,894 alleles
Filtering AF
0.0147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0113%
Overall
0.00571%
80/1,401,054 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0263% | 3,809 |
| Admixed American | 0.0172% | 5,829 |
| South Asian | 0.0127% | 7,865 |
| Remaining individualsnot grpmax-eligible | 0.00727% | 13,752 |
| African / African-American | 0.00437% | 22,871 |
| European (non-Finnish) | 0.00402% | 24,859 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00352% | 28,412 |
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.Ser1030=
- Coding
- c.3090G>A
- MANE Select
- NM_004327
- dbSNP
- rs766103643
- Type
- single nucleotide variant
- Location
- chr22:23310341 (GRCh38)
- Gene constraint
- LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.61 · 5 PDB
Similar variants
- BCR p.Ser1030Leu 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-ser1030 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown