ALG9 c.895+322T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 27.2%, 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 | ||
| Splice region | donor +322 | deep intronic (+322 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP -0.47 |
| Non-coding constraint | Z -0.06 | 1 kb window · o/e 1.00 · regional · uncalibrated |
| Overall | ||
| CADD | 5.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
27.2%
African / African-American · 11,117/40,922 alleles
Filtering AF
26.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 26.6%
Overall
7.89%
11,812/149,778 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 27.2% | 4 |
| Remaining individualsnot grpmax-eligible | 5.88% | 17 |
| Admixed American | 3.32% | 30 |
| Middle Eastern | 0.69% | 145 |
| European (non-Finnish) | 0.11% | 912 |
| South Asian | 0.0646% | 1,549 |
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.895+322T>C
- MANE Select
- NM_024740
- dbSNP
- rs73558072
- Type
- single nucleotide variant
- Location
- chr11:111853058 (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-895-plus-322t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown