ALG9 c.895+299del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 59.2%, eas) — 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 +299 | deep intronic (+299 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.25 | GERP -2.7 |
| Non-coding constraint | Z -0.06 | 1 kb window · o/e 1.00 · regional · uncalibrated |
| Overall | ||
| CADD | 0.029 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
59.2%
East Asian · 2,946/4,974 alleles
Filtering AF
57.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 56.7%
Overall
38.9%
54,588/140,218 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 59.2% | 2 |
| Amishnot grpmax-eligible | 56.9% | 2 |
| African / African-American | 43.4% | 2 |
| Middle Eastern | 43.2% | 2 |
| Finnishnot grpmax-eligible | 40.4% | 2 |
| South Asian | 40.3% | 2 |
| Admixed American | 36.2% | 3 |
| Remaining individualsnot grpmax-eligible | 35.9% | 3 |
| European (non-Finnish) | 35.4% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 27.1% | 4 |
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+299del
- MANE Select
- NM_024740
- dbSNP
- rs200952010
- Type
- Deletion
- Location
- chr11:111853081 (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-895-plus-299del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown