ALG9 c.-26C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0205%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.65 | GERP -5 |
| Non-coding constraint | Z -0.88 | 1 kb window · o/e 1.06 · regional · uncalibrated |
| Overall | ||
| CADD | 4.782 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0205%
African / African-American · 15/73,090 alleles
Filtering AF
0.0126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00983%
151/1,535,396 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0205% | 4,873 |
| European (non-Finnish) | 0.0111% | 9,026 |
| Remaining individualsnot grpmax-eligible | 0.00667% | 14,991 |
| East Asian | 0.0049% | 20,413 |
| South Asian | 0.00358% | 27,903 |
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.-26C>T
- MANE Select
- NM_024740
- dbSNP
- rs570877727
- Type
- single nucleotide variant
- Location
- chr11:111871508 (GRCh38)
- Gene constraint
- LOEUF 0.853 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.35 · 2 PDB
Similar variants
- ALG9 c.566-1G>A Pathogenic/Likely pathogenic ★★ same type
- ALG9 c.896-2A>G Likely pathogenic ★★ same type
- ALG9 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same type
- ALG9 p.Trp248Ter Pathogenic/Likely pathogenic ★★ same type
- ALG9 p.Tyr287Cys Pathogenic/Likely pathogenic ★★ same type
- ALG9 c.*1607C>T Uncertain significance ★★ same type
- ALG9 c.*1624A>C Uncertain significance ★★ same type
- ALG9 c.*1722C>T 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-minus-26c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown