Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.8%, afr) — 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 -0.14 | GERP -2.9, phastCons 0.001 |
| Overall | ||
| CADD | 1.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.8%
African / African-American · 7,340/74,920 alleles
Filtering AF
9.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.53%
Overall
0.539%
8,703/1,613,538 alleles · common
exomes 4,419/1,461,436 · genomes 4,284/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.8% | 10 |
| Admixed American | 0.917% | 109 |
| Remaining individualsnot grpmax-eligible | 0.807% | 124 |
| Middle Eastern | 0.554% | 181 |
| European (non-Finnish) | 0.022% | 4,538 |
| South Asian | 0.0165% | 6,070 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,592 |
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
- CDH7
- Protein
- p.Glu28=
- Coding
- c.84A>G
- MANE Select
- NM_004361
- dbSNP
- rs7229292
- Type
- single nucleotide variant
- Location
- chr18:65762926 (GRCh38)
- Structure
- AlphaFold pLDDT 78.14
Similar variants
- CDH19 p.Pro558= Benign ★★ same type
- CDH19 p.Thr89Ile Benign ★★ same type
- CDH7 c.1612+22C>T Benign ★★ same type
- CDH7 c.1612+24A>T Benign ★★ same type
- CDH7 c.1612+81T>C Benign ★★ same type
- CDH7 c.1864+225A>G Benign ★★ same type
- CDH7 c.210+52G>A Benign ★★ same type
- CDH7 c.210+56T>G Benign ★★ 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/cdh7-p-glu28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown