BAZ2A p.Gln118=
c.354A>G · VCV3479838
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, 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 -8.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.295 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,962 alleles
Filtering AF
0.00544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00242%
39/1,613,174 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,566 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,491 |
| East Asian | 0.00446% | 22,426 |
| African / African-American | 0.00401% | 24,927 |
| South Asian | 0.0022% | 45,523 |
| European (non-Finnish) | 0.0017% | 58,987 |
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
- BAZ2A
- Protein
- p.Gln118=
- Coding
- c.354A>G
- MANE Select
- NM_001300905
- Type
- single nucleotide variant
- Location
- chr12:56615390 (GRCh38)
- Gene constraint
- LOEUF 0.226 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.27 · 67 PDB
Similar variants
- BAZ2A p.Ala1061Pro Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1111Ser Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1160Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1223Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1229Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala142Thr Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1770Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala17Val 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/baz2a-p-gln118 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown