ALG9 c.*2479del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 8.31%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -1.3, phastCons 0.003 |
| Non-coding constraint | Z 0.87 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 0.042 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.31%
African / African-American · 2,639/31,762 alleles
Filtering AF
8.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.94%
Overall
2.73%
3,171/116,202 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.31% | 12 |
| South Asian | 6.07% | 16 |
| Remaining individualsnot grpmax-eligible | 2.4% | 42 |
| Middle Eastern | 2.31% | 43 |
| Admixed American | 1.2% | 83 |
| East Asian | 0.786% | 127 |
| European (non-Finnish) | 0.184% | 544 |
| Finnishnot grpmax-eligible | 0.0936% | 1,069 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0744% | 1,344 |
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
- ALG9
- Coding
- c.*2479del
- MANE Select
- NM_024740
- dbSNP
- rs376955296
- Type
- Deletion
- Location
- chr11:111783918 (GRCh38)
- Gene constraint
- LOEUF 0.853 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.35 · 2 PDB
Similar variants
- ALG9 p.Arg409fs Pathogenic/Likely pathogenic ★★ same type
- ALG9 c.1605_1608del Likely pathogenic ★ same type
- ALG9 c.896_1602del Pathogenic ★ same type
- ALG9 p.Ala175fs Likely pathogenic ★ same type
- ALG9 p.Leu235fs Likely pathogenic ★ same type
- ALG9 p.Met331fs Pathogenic ★ same type
- ALG9 p.Thr43fs Pathogenic ★ same type
- ALG9 c.*1679del 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/alg9-c-star-2479del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown