Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 84.8%, amr) — 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 -9 | GERP -3.7 |
| Overall | ||
| CADD | 0.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
84.8%
Admixed American · 50,922/60,020 alleles
Filtering AF
84.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 84%
Overall
80.7%
1,302,611/1,613,744 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 84.8% | 1 |
| African / African-American | 83.3% | 1 |
| Middle Eastern | 82.7% | 1 |
| South Asian | 81.2% | 1 |
| Finnishnot grpmax-eligible | 80.6% | 1 |
| European (non-Finnish) | 80.4% | 1 |
| Remaining individualsnot grpmax-eligible | 80.2% | 1 |
| East Asian | 79.9% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 78.3% | 1 |
| Amishnot grpmax-eligible | 76.4% | 1 |
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
- CDH13
- Protein
- p.Ala692=
- Coding
- c.2076A>G
- MANE Select
- NM_001257
- dbSNP
- rs1048612
- Type
- single nucleotide variant
- Location
- chr16:83783414 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.19 · 1 PDB
- Residue 692
- the cadherin 5 domain
Similar variants
- CDH13 p.Ala692Val Uncertain significance ★ ⚠ same residue
- CDH13 c.1102-6T>C Benign ★★ same type
- CDH13 c.1284+90A>G Benign ★★ same type
- CDH13 c.1539-109T>C Benign ★★ same type
- CDH13 c.1681+64T>C Benign ★★ same type
- CDH13 c.1682-151C>T Benign ★★ same type
- CDH13 c.1682-180G>A Benign ★★ same type
- CDH13 c.1682-59A>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/cdh13-p-ala692 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown