ALG1 c.390+207C>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.04%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +207 | deep intronic (+207 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -2.4 |
| Overall | ||
| CADD | 0.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.04%
African / African-American · 2,192/54,284 alleles
Filtering AF
3.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.84%
Overall
0.414%
2,535/612,984 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.04% | 25 |
| Middle Eastern | 0.524% | 191 |
| Remaining individualsnot grpmax-eligible | 0.417% | 240 |
| Admixed American | 0.302% | 331 |
| European (non-Finnish) | 0.0287% | 3,483 |
| South Asian | 0.00773% | 12,934 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00565% | 17,714 |
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
- ALG1
- Coding
- c.390+207C>G
- MANE Select
- NM_019109
- dbSNP
- rs112467044
- Type
- single nucleotide variant
- Location
- chr16:5073463 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.24
Similar variants
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- ALG1 c.1187+2T>C Pathogenic ★★ same type
- ALG1 c.1188-2A>G Pathogenic/Likely pathogenic ★★ same type
- ALG1 c.209-2A>G Likely pathogenic ★★ same type
- ALG1 c.539+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALG1 c.630-2A>G Likely pathogenic ★★ same type
- ALG1 c.863-2A>G Likely pathogenic ★★ same type
- ALG1 c.961+1G>A 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/alg1-c-390-plus-207c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown