ALG1 c.901+71C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 65.6%, sas) — 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 +71 | deep intronic (+71 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -2.7 |
| Non-coding constraint | Z -0.05 | 1 kb window · o/e 1.00 · regional · uncalibrated |
| Overall | ||
| CADD | 1.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
65.6%
South Asian · 57,887/88,278 alleles
Filtering AF
65.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 64.9%
Overall
52.1%
815,924/1,565,058 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 65.6% | 2 |
| East Asian | 62.1% | 2 |
| Finnishnot grpmax-eligible | 56.4% | 2 |
| Remaining individualsnot grpmax-eligible | 52.3% | 2 |
| European (non-Finnish) | 51.5% | 2 |
| Amishnot grpmax-eligible | 51.3% | 2 |
| African / African-American | 48.3% | 2 |
| Middle Eastern | 47.2% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 46.1% | 2 |
| Admixed American | 40.7% | 2 |
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.901+71C>T
- MANE Select
- NM_019109
- dbSNP
- rs1846688
- Type
- single nucleotide variant
- Location
- chr16:5079173 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.24
Similar variants
- ALG1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same type
- 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-901-plus-71c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown