BST2 p.Ala130=
c.390G>A · VCV4216597
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00348%, amr)
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 -8.9 | GERP -2 |
| Overall | ||
| CADD | 2.627 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00348%
Admixed American · 2/57,520 alleles
Filtering AF
0.000577%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000216%
Overall
0.000563%
9/1,597,534 alleles · very rare
exomes 8/1,445,486 · genomes 1/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00348% | 28,760 |
| South Asian | 0.00225% | 44,389 |
| African / African-American | 0.00134% | 74,436 |
| European (non-Finnish) | 0.000341% | 292,994 |
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
- BST2
- Protein
- p.Ala130=
- Coding
- c.390G>A
- MANE Select
- NM_004335
- Type
- single nucleotide variant
- Location
- chr19:17404152 (GRCh38)
- Gene constraint
- LOEUF 0.969 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.63 · 15 PDB
- Residue 130
- an α-helix
Similar variants
- BST2 p.Ala107Asp Uncertain significance ★ ⚠ same type
- BST2 p.Ala163Thr Uncertain significance ★ ⚠ same type
- BST2 p.Ala177Pro Uncertain significance ★ ⚠ same type
- BST2 p.Arg10Ser Uncertain significance ★ ⚠ same type
- BST2 p.Arg147Thr Uncertain significance ★ ⚠ same type
- BST2 p.Arg19Cys Uncertain significance ★ ⚠ same type
- BST2 p.Arg19Gly Uncertain significance ★ ⚠ same type
- BST2 p.Arg58Trp 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/bst2-p-ala130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown