CDH13 c.960+183C>G
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 13.8%, 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 | ||
| Splice region | donor +183 | deep intronic (+183 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP 1.1 |
| Non-coding constraint | Z 1.76 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 2.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
13.8%
African / African-American · 5,732/41,448 alleles
Filtering AF
13.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.4%
Overall
4.02%
6,120/152,120 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 13.8% | 7 |
| Remaining individualsnot grpmax-eligible | 2.84% | 35 |
| Middle Eastern | 2.4% | 42 |
| Admixed American | 1.47% | 68 |
| Ashkenazi Jewishnot grpmax-eligible | 0.807% | 124 |
| European (non-Finnish) | 0.0941% | 1,063 |
| South Asian | 0.0831% | 1,203 |
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
- Coding
- c.960+183C>G
- MANE Select
- NM_001257
- dbSNP
- rs16960646
- Type
- single nucleotide variant
- Location
- chr16:83486838 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.19 · 1 PDB
Similar variants
- 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
- CDH13 c.1682-62G>A 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-c-960-plus-183c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown