Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.51%, 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 -1.6 | GERP -3.3 |
| Overall | ||
| CADD | 0.911 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.51%
African / African-American · 2,636/75,064 alleles
Filtering AF
3.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.35%
Overall
0.191%
3,081/1,614,198 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.51% | 28 |
| Remaining individualsnot grpmax-eligible | 0.277% | 361 |
| Admixed American | 0.255% | 392 |
| Middle Eastern | 0.214% | 466 |
| European (non-Finnish) | 0.00856% | 11,684 |
| South Asian | 0.00549% | 18,218 |
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
- APBB1
- Protein
- p.Asn126=
- Coding
- c.378C>T
- MANE Select
- NM_001164
- dbSNP
- rs2682094
- Type
- single nucleotide variant
- Location
- chr11:6410970 (GRCh38)
- Gene constraint
- LOEUF 0.401 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 60.75 · 11 PDB
Similar variants
- SMPD1 p.Arg498Leu Pathogenic ★★ same type
- APBB1 p.Ala371= Benign ★★ same type
- APBB1 p.Arg51Cys Benign ★★ ⚠ same type
- APBB1 p.Leu385= Benign ★★ same type
- APBB1 p.Met327Val Likely benign ★★ same type
- APBB1 c.721+1G>T Uncertain significance ★ same type
- APBB1 p.Ala157Val Uncertain significance ★ ⚠ same type
- APBB1 p.Ala194Asp Uncertain significance ★ ⚠ 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/apbb1-p-asn126 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown