ADGRE2 p.Cys693=
c.2079C>T · rs61732001 · VCV782624
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.4%, afr)
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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 1.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.4%
African / African-American · 2,552/74,954 alleles
Filtering AF
3.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.25%
Overall
0.183%
2,958/1,613,710 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.4% | 29 |
| Remaining individualsnot grpmax-eligible | 0.274% | 365 |
| Admixed American | 0.24% | 416 |
| Middle Eastern | 0.149% | 673 |
| East Asian | 0.00669% | 14,957 |
| European (non-Finnish) | 0.00636% | 15,732 |
| South Asian | 0.00439% | 22,756 |
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
- ADGRE2
- Protein
- p.Cys693=
- Coding
- c.2079C>T
- MANE Select
- NM_013447
- dbSNP
- rs61732001
- Type
- single nucleotide variant
- Location
- chr19:14746908 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.44 · 3 PDB
Similar variants
- ADGRE2 p.Cys693Ter Uncertain significance ★ same residue
- ADGRE2 p.Ala359Gly Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala44Thr Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala554Val Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala555Ser Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala589Thr Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala603Thr Uncertain significance ★★ ⚠ same type
- ADGRE2 p.Ala656Thr 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/adgre2-p-cys693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown