ALG6 c.82+76A>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.86%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +76 | deep intronic (+76 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -5.1 |
| Non-coding constraint | Z 1.15 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 5.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.86%
South Asian · 3,779/77,710 alleles
Filtering AF
4.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.68%
Overall
1.64%
16,282/991,784 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 4.86% | 21 |
| African / African-American | 3.65% | 27 |
| Middle Eastern | 3.3% | 30 |
| Remaining individualsnot grpmax-eligible | 1.58% | 63 |
| European (non-Finnish) | 1.36% | 73 |
| Ashkenazi Jewishnot grpmax-eligible | 1.31% | 77 |
| Admixed American | 0.934% | 107 |
| Finnishnot grpmax-eligible | 0.153% | 653 |
| East Asian | 0.00478% | 20,939 |
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
- ALG6
- Coding
- c.82+76A>G
- MANE Select
- NM_013339
- dbSNP
- rs11579622
- Type
- single nucleotide variant
- Location
- chr1:63371135 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.08
Similar variants
- ALG6 c.1128-1G>A Likely pathogenic ★★ same type
- ALG6 c.1128-2A>C Likely pathogenic ★★ same type
- ALG6 c.1326+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALG6 c.257+5G>A Pathogenic/Likely pathogenic ★★ same type
- ALG6 c.429+1G>T Likely pathogenic ★★ same type
- ALG6 c.495-2A>G Likely pathogenic ★★ same type
- ALG6 c.495-2A>T Likely pathogenic ★★ same type
- ALG6 c.680+1G>A Pathogenic/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/alg6-c-82-plus-76a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown