BACE2 p.Ala37=
c.111G>A · rs369963511 · VCV3048890
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.982%, afr)
Conditions
1
BACE2-related disorder
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 0.22 | GERP -0.99, phastCons 0.006 |
| Overall | ||
| CADD | 7.595 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.982%
African / African-American · 648/65,996 alleles
Filtering AF
0.919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.894%
Overall
0.0686%
959/1,398,120 alleles · rare
exomes 490/1,246,542 · genomes 469/151,578 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.982% | 102 |
| Remaining individualsnot grpmax-eligible | 0.0975% | 1,025 |
| Admixed American | 0.0752% | 1,329 |
| Middle Eastern | 0.0517% | 1,933 |
| South Asian | 0.037% | 2,700 |
| East Asian | 0.0308% | 3,243 |
| European (non-Finnish) | 0.0183% | 5,473 |
| Finnishnot grpmax-eligible | 0.00757% | 13,204 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00432% | 23,160 |
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
- BACE2
- Protein
- p.Ala37=
- Coding
- c.111G>A
- MANE Select
- NM_012105
- dbSNP
- rs369963511
- Type
- single nucleotide variant
- Location
- chr21:41168374 (GRCh38)
- Gene constraint
- LOEUF 0.574 · pLI 0.73 (gnomAD)
- Structure
- AlphaFold pLDDT 83.31 · 19 PDB
Disease context
BACE2-related disorder
Similar variants
- BACE2 c.748-10C>T Benign same condition
- BACE2 p.Ala460Thr Likely benign same condition
- BACE2 p.Asp364= Benign same condition
- PLAC4 n.5627C>T Likely benign same condition
- BACE2 c.1135-10C>T Benign ★★ same type
- BACE2 c.1304-8C>T Benign ★★ same type
- BACE2 p.His56Tyr Benign ★★ same type
- BACE2 p.Ser88= 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/bace2-p-ala37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown