SNAP29 p.Ala37=
c.111G>T · rs760763995 · VCV2969827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0145%, sas)
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 -1 | |
| Overall | ||
| CADD | 2.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0145%
South Asian · 13/89,894 alleles
Filtering AF
0.00855%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00669%
Overall
0.0015%
24/1,604,540 alleles · ultra-rare
exomes 23/1,452,340 · genomes 1/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0145% | 6,915 |
| East Asian | 0.00224% | 44,624 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,080 |
| European (non-Finnish) | 0.000765% | 130,740 |
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
- SNAP29
- Protein
- p.Ala37=
- Coding
- c.111G>T
- MANE Select
- NM_004782
- dbSNP
- rs760763995
- Type
- single nucleotide variant
- Location
- chr22:20859221 (GRCh38)
- Gene constraint
- LOEUF 0.833 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.85 · 2 PDB
- Residue 37
- the 'disordered' region
Similar variants
- SNAP29 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same type
- SNAP29 p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
- SNAP29 c.-76G>A Uncertain significance ★★ same type
- SNAP29 c.*3014C>T Uncertain significance ★★ same type
- SNAP29 c.*840G>C Uncertain significance ★★ same type
- SNAP29 p.Ala20Pro Uncertain significance ★★ ⚠ same type
- SNAP29 p.Ala65Pro Uncertain significance ★★ ⚠ same type
- SNAP29 p.Arg215Cys 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/snap29-p-ala37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown