ADGRE2 p.Phe282=
c.846C>T · rs79043020 · VCV786666
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.32%, 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 -13 | GERP -2.7 |
| Overall | ||
| CADD | 3.787 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.32%
African / African-American · 989/75,056 alleles
Filtering AF
1.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
0.085%
1,372/1,614,166 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.32% | 76 |
| Ashkenazi Jewishnot grpmax-eligible | 0.611% | 164 |
| Remaining individualsnot grpmax-eligible | 0.173% | 579 |
| Admixed American | 0.0883% | 1,132 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00439% | 22,772 |
| European (non-Finnish) | 0.00297% | 33,715 |
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.Phe282=
- Coding
- c.846C>T
- MANE Select
- NM_013447
- dbSNP
- rs79043020
- Type
- single nucleotide variant
- Location
- chr19:14765380 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.44 · 3 PDB
Similar variants
- 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
- ADGRE2 p.Ala664Gly 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-phe282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown