CDH7 p.Lys2=
c.6G>A · rs114985920 · VCV714874
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.98%, 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 12 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 12.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.98%
African / African-American · 731/74,580 alleles
Filtering AF
0.921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.898%
Overall
0.0536%
860/1,605,906 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.98% | 102 |
| Remaining individualsnot grpmax-eligible | 0.0708% | 1,411 |
| Admixed American | 0.0524% | 1,910 |
| South Asian | 0.00453% | 22,074 |
| European (non-Finnish) | 0.00425% | 23,548 |
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.Lys2=
- Coding
- c.6G>A
- MANE Select
- NM_021153 · reported on NM_004361
- dbSNP
- rs114985920
- Type
- single nucleotide variant
- Location
- chr18:65762848 (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-lys2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown