ALG3 c.52+9G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.16%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.92 | GERP -3.2, phastCons 0.002 |
| Non-coding constraint | Z 3.04 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 3.799 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.16%
East Asian · 522/44,840 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.05%
Overall
0.0532%
858/1,612,358 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.16% | 86 |
| African / African-American | 0.361% | 277 |
| Remaining individualsnot grpmax-eligible | 0.0769% | 1,301 |
| Admixed American | 0.0151% | 6,644 |
| European (non-Finnish) | 0.000678% | 147,420 |
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
- ALG3
- Coding
- c.52+9G>A
- MANE Select
- NM_005787 · reported on NM_001006941
- dbSNP
- rs76371354
- Type
- single nucleotide variant
- Location
- chr3:184249217 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Similar variants
- ALG3 c.444+1G>T Likely pathogenic ★★ same type
- ALG3 p.Arg171Gln Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Arg266Cys Pathogenic ★★ same type
- ALG3 p.Arg354Cys Likely pathogenic ★★ same type
- ALG3 p.Arg354His Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Asn174Ser Likely pathogenic ★★ ⚠ same type
- ALG3 p.Gly55= Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Ile69Thr Likely pathogenic ★★ 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/alg3-c-52-plus-9g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown