BCAT2 p.Ala163=
c.489C>A · rs377190765 · VCV1176713
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.116%, mid)
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 -20 | GERP -4.1 |
| Overall | ||
| CADD | 0.002 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.116%
Middle Eastern · 7/6,060 alleles
Filtering AF
0.0812%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0752%
Overall
0.0182%
293/1,613,570 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.116% | 866 |
| South Asian | 0.0977% | 1,023 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,674 |
| European (non-Finnish) | 0.0151% | 6,629 |
| Admixed American | 0.00167% | 60,014 |
| Finnishnot grpmax-eligible | 0.00157% | 63,630 |
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
- BCAT2
- Protein
- p.Ala163=
- Coding
- c.489C>A
- MANE Select
- NM_001190
- dbSNP
- rs377190765
- Type
- single nucleotide variant
- Location
- chr19:48800023 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.47 · 30 PDB
- Residue 163
- a β-strand
Similar variants
- BCAT2 p.Ala188Thr Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg133His Uncertain significance ★★ same type
- BCAT2 p.Arg247Trp Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg325Trp Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg333Gly Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg371His Uncertain significance ★★ ⚠ same type
- BCAT2 p.Asp112Asn Uncertain significance ★★ ⚠ same type
- BCAT2 p.Asp259Asn 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/bcat2-p-ala163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown