Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 86.6%, 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 | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -3.1 |
| Overall | ||
| CADD | 0.076 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
86.6%
East Asian · 37,013/42,752 alleles
Filtering AF
85.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 85.5%
Overall
56.6%
895,010/1,581,660 alleles · common
exomes 797,677/1,429,532 · genomes 97,333/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 86.6% | 1 |
| African / African-American | 85.3% | 1 |
| Remaining individualsnot grpmax-eligible | 58.5% | 2 |
| Finnishnot grpmax-eligible | 57.3% | 2 |
| South Asian | 54.8% | 2 |
| Middle Eastern | 54.5% | 2 |
| European (non-Finnish) | 54.1% | 2 |
| Amishnot grpmax-eligible | 52.7% | 2 |
| Admixed American | 52.3% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 48.3% | 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
- LIG1
- Protein
- p.Asp802=
- Coding
- c.2406T>C
- MANE Select
- NM_000234
- dbSNP
- rs20581
- Type
- single nucleotide variant
- Location
- chr19:48119170 (GRCh38)
- Structure
- AlphaFold pLDDT 75.13 · 2 PDB
Similar variants
- LIG1 p.Ala269Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala293Val Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala412Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala443Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala462Ser Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala545Gly Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala578Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala708Thr 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/lig1-p-asp802 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown