ALG12 c.162+22del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.69%, 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 +22 | near-intronic (+22 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.92 | GERP -0.45 |
| Overall | ||
| CADD | 0.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.69%
African / African-American · 4,269/75,022 alleles
Filtering AF
5.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.49%
Overall
0.309%
4,980/1,613,978 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.69% | 18 |
| Admixed American | 0.495% | 202 |
| Remaining individualsnot grpmax-eligible | 0.435% | 230 |
| Middle Eastern | 0.247% | 404 |
| European (non-Finnish) | 0.0103% | 9,672 |
| South Asian | 0.00549% | 18,216 |
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
- ALG12
- Coding
- c.162+22del
- MANE Select
- NM_024105
- dbSNP
- rs201822626
- Type
- Deletion
- Location
- chr22:49913582 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.26
Similar variants
- ALG12 p.Arg311fs Pathogenic ★★ same type
- ALG12 p.Asn334fs Pathogenic/Likely pathogenic ★★ same type
- ALG12 p.Gln40fs Pathogenic ★★ same type
- ALG12 p.Leu12fs Pathogenic/Likely pathogenic ★★ same type
- ALG12 p.Lys416fs Likely pathogenic ★★ same type
- ALG12 p.Arg486fs Uncertain significance ★★ same type
- ALG12 c.439_469+19del Likely pathogenic ★ same type
- ALG12 c.664+1_664+9del 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/alg12-c-162-plus-22del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown