BAX c.474+34C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.074 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +34 | near-intronic (+34 nt from the splice site) |
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | |
| Non-coding constraint | Z 2.81 | 1 kb window · o/e 0.82 · regional · uncalibrated |
| Overall | ||
| CADD | 4.918 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
South Asian · 28/91,064 alleles
Filtering AF
0.0218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0188%
Overall
0.00378%
61/1,613,112 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0307% | 3,252 |
| Admixed American | 0.00833% | 12,000 |
| African / African-American | 0.00667% | 14,998 |
| East Asian | 0.00446% | 22,422 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,233 |
| European (non-Finnish) | 0.00161% | 62,100 |
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
- BAX
- Coding
- c.474+34C>T
- MANE Select
- NM_138761
- Type
- single nucleotide variant
- Location
- chr19:48960948 (GRCh38)
- Gene constraint
- LOEUF 1.245 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.71 · 37 PDB
Similar variants
- BAX p.Asp102= Benign ★★ same type
- BAX c.474+151G>A Uncertain significance ★ same type
- BAX c.474+20C>A Uncertain significance ★ same type
- BAX c.474+76G>A Uncertain significance ★ same type
- BAX c.474+95G>C Uncertain significance ★ same type
- BAX p.Ala81Pro Uncertain significance ★ ⚠ same type
- BAX p.Arg134Gly Uncertain significance ★ ⚠ same type
- BAX p.Arg145Gln 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/bax-c-474-plus-34c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown