BAIAP2 p.Ala119=
c.357G>A · VCV3985238
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0512%, 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 -7.2 | GERP -3.9 |
| Overall | ||
| CADD | 2.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0512%
East Asian · 23/44,890 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00335%
54/1,613,798 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0512% | 1,952 |
| European (non-Finnish) | 0.00246% | 40,685 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| African / African-American | 0.00133% | 74,912 |
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
- BAIAP2
- Protein
- p.Ala119=
- Coding
- c.357G>A
- MANE Select
- NM_001144888
- Type
- single nucleotide variant
- Location
- chr17:81086448 (GRCh38)
- Gene constraint
- LOEUF 0.446 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.81 · 12 PDB
- Residue 119
- the imd domain; an α-helix
Similar variants
- BAIAP2 c.1269-7C>T Likely benign ★★ same type
- BAIAP2 c.643-9C>T Benign ★★ same type
- BAIAP2 p.Gln449= Benign ★★ same type
- BAIAP2 p.Pro522= Benign/Likely benign ★★ same type
- BAIAP2 p.Thr185= Benign ★★ same type
- BAIAP2 p.Val204= Benign ★★ same type
- BAIAP2 c.1535+1763T>G Uncertain significance ★ same type
- BAIAP2 c.1535+553G>A 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/baiap2-p-ala119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown