Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, afr)
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 -1.1 | GERP -2.5, phastCons 0.004 |
| Overall | ||
| CADD | 1.388 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
African / African-American · 834/57,102 alleles
Filtering AF
1.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.078%
943/1,209,232 alleles · low-frequency
exomes 509/1,097,690 · genomes 434/111,542 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.46% | 68 |
| Admixed American | 0.12% | 830 |
| Remaining individualsnot grpmax-eligible | 0.0987% | 1,013 |
| Middle Eastern | 0.023% | 4,353 |
| South Asian | 0.00352% | 28,386 |
| European (non-Finnish) | 0.000447% | 223,675 |
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
- AGTR2
- Protein
- p.Leu166=
- Coding
- c.498T>C
- MANE Select
- NM_000686
- dbSNP
- rs5190
- Type
- single nucleotide variant
- Location
- chrX:116172778 (GRCh38)
- Structure
- AlphaFold pLDDT 82.34 · 7 PDB
- Residue 166
- an α-helix
Similar variants
- AGTR2 p.His237Gln Uncertain significance ★★ ⚠ same type
- AGTR2 p.Arg248Lys Benign ★★ same type
- AGTR2 p.Gly21Val Benign/Likely benign ★★ same type
- AGTR2 p.Ile337= Benign ★★ same type
- AGTR2 p.Ala171Val Uncertain significance ★ ⚠ same type
- AGTR2 p.Ala212Gly Uncertain significance ★ ⚠ same type
- AGTR2 p.Asn29Ser Uncertain significance ★ ⚠ same type
- AGTR2 p.Asn310Lys 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/agtr2-p-leu166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown