BAIAP3 p.Phe244=
c.732C>T · VCV4193622
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.436%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.6, phastCons 0.001 |
| Overall | ||
| CADD | 6.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.436%
African / African-American · 327/75,014 alleles
Filtering AF
0.397%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.382%
Overall
0.0236%
381/1,612,302 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.436% | 229 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,974 |
| Admixed American | 0.0267% | 3,748 |
| East Asian | 0.00223% | 44,856 |
| European (non-Finnish) | 0.00136% | 73,733 |
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
- BAIAP3
- Protein
- p.Phe244=
- Coding
- c.732C>T
- MANE Select
- NM_001199097
- Type
- single nucleotide variant
- Location
- chr16:1341822 (GRCh38)
- Gene constraint
- LOEUF 1.406 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.27
- Residue 244
- the c2 1 domain
Similar variants
- BAIAP3 p.Phe244Leu Uncertain significance ★ ⚠ same residue
- BAIAP3 c.-11+926G>T Uncertain significance ★ ⚠ same type
- BAIAP3 c.-11+983T>A Uncertain significance ★ ⚠ same type
- BAIAP3 c.-11+985G>A Uncertain significance ★ ⚠ same type
- BAIAP3 c.-11+991G>A Uncertain significance ★ ⚠ same type
- BAIAP3 c.-11+996C>G Uncertain significance ★ ⚠ same type
- BAIAP3 c.-6C>T Uncertain significance ★ ⚠ same type
- BAIAP3 p.Ala1007Gly 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/baiap3-p-phe244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown