Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 9.1%, 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 -16 | GERP -4.9 |
| Overall | ||
| CADD | 0.011 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.1%
African / African-American · 6,805/74,774 alleles
Filtering AF
8.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.85%
Overall
0.479%
7,706/1,609,634 alleles · common
exomes 3,844/1,457,812 · genomes 3,862/151,822 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.1% | 11 |
| Admixed American | 0.641% | 156 |
| Remaining individualsnot grpmax-eligible | 0.623% | 161 |
| Middle Eastern | 0.265% | 377 |
| South Asian | 0.0231% | 4,334 |
| European (non-Finnish) | 0.00782% | 12,788 |
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.Pro163=
- Coding
- c.489C>G
- MANE Select
- NM_004361
- dbSNP
- rs7235166
- Type
- single nucleotide variant
- Location
- chr18:65809982 (GRCh38)
- Structure
- AlphaFold pLDDT 78.14
- Residue 163
- the cadherin 2 domain
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-pro163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown