BAIAP2 p.Val204=
c.612G>A · rs111402402 · VCV711694
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.9%, 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 8.5 | GERP 0.42, phastCons 1 |
| Overall | ||
| CADD | 12.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.9%
African / African-American · 1,428/75,034 alleles
Filtering AF
1.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.79%
Overall
0.11%
1,779/1,612,134 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.9% | 53 |
| Admixed American | 0.263% | 380 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| Middle Eastern | 0.0713% | 1,403 |
| European (non-Finnish) | 0.00585% | 17,098 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
| South Asian | 0.0022% | 45,528 |
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.Val204=
- Coding
- c.612G>A
- MANE Select
- NM_001144888
- dbSNP
- rs111402402
- Type
- single nucleotide variant
- Location
- chr17:81100050 (GRCh38)
- Gene constraint
- LOEUF 0.446 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.81 · 12 PDB
- Residue 204
- 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 c.1535+1763T>G Uncertain significance ★ same type
- BAIAP2 c.1535+553G>A Uncertain significance ★ same type
- BAIAP2 c.490-1717A>G 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-val204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown