Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 13 submitters
gnomAD v4.1
Common
common (popmax 92.3%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
focal segmental glomerulosclerosis 5
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.5 | GERP 2.7 |
| Overall | ||
| CADD | 1.133 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
92.3%
East Asian · 39,462/42,772 alleles
Filtering AF
91.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 91.2%
Overall
77.2%
1,201,217/1,556,818 alleles · common
exomes 1,079,694/1,404,700 · genomes 121,523/152,118 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 92.3% | 1 |
| African / African-American | 87.1% | 1 |
| Admixed American | 84.4% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 80% | 1 |
| Remaining individualsnot grpmax-eligible | 78.2% | 1 |
| Middle Eastern | 77.8% | 1 |
| European (non-Finnish) | 75.9% | 1 |
| Finnishnot grpmax-eligible | 73.7% | 1 |
| South Asian | 73.5% | 1 |
| Amishnot grpmax-eligible | 72% | 1 |
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
- INF2
- Protein
- p.Asp1022=
- Coding
- c.3066T>C
- MANE Select
- NM_022489
- dbSNP
- rs4983535
- Type
- single nucleotide variant
- Location
- chr14:104714228 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.34 · 10 PDB
- Residue 1022
- the 'disordered' region
Similar variants
- INF2 p.Asp1022Glu Uncertain significance ★★ ⚠ same residue
- INF2 p.Arg177Cys Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg214Cys Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg214His Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg218Gln Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg218Trp Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg91Gly Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Asn202Asp Likely pathogenic ★★ same condition
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/inf2-p-asp1022 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown