CDH23 c.2176+12del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00406%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +12 | near-intronic (+12 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.5 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 9.793 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00406%
African / African-American · 3/73,942 alleles
Filtering AF
0.00108%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000732%
Overall
0.00146%
23/1,574,440 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00406% | 24,647 |
| Admixed American | 0.00177% | 56,440 |
| Finnishnot grpmax-eligible | 0.00162% | 61,900 |
| European (non-Finnish) | 0.00147% | 68,015 |
| South Asian | 0.00116% | 85,932 |
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
- CDH23
- Coding
- c.2176+12del
- MANE Select
- NM_022124
- dbSNP
- rs770990654
- Type
- Deletion
- Location
- chr10:71690590 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- CDH23 c.1143_1176del Pathogenic/Likely pathogenic ★★ same type
- CDH23 c.336+1del Likely pathogenic ★★ same type
- CDH23 c.9280_9286del Pathogenic/Likely pathogenic ★★ same type
- CDH23 p.Ala2232_Val2233insTer Pathogenic/Likely pathogenic ★★ same type
- CDH23 p.Ala2309fs Pathogenic/Likely pathogenic ★★ same type
- CDH23 p.Ala2685fs Pathogenic ★★ same type
- CDH23 p.Arg2115fs Pathogenic/Likely pathogenic ★★ same type
- CDH23 p.Asn1889fs Likely pathogenic ★★ 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/cdh23-c-2176-plus-12del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown