CDON c.2158+7A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00433%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.03 | GERP -2.3 |
| Non-coding constraint | Z 1.34 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 3.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00433%
European (non-Finnish) · 51/1,178,964 alleles
Filtering AF
0.00334%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00302%
Overall
0.00341%
55/1,612,634 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00433% | 23,117 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,203 |
| African / African-American | 0.00267% | 37,427 |
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
- CDON
- Coding
- c.2158+7A>C
- MANE Select
- NM_001378964
- dbSNP
- rs376244204
- Type
- single nucleotide variant
- Location
- chr11:126001712 (GRCh38)
- Gene constraint
- LOEUF 0.733 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.62 · 3 PDB
Similar variants
- CDON c.3276+1G>T Uncertain significance ★★ same type
- CDON c.640+1G>A Uncertain significance ★★ same type
- CDON c.*1805A>G Uncertain significance ★★ same type
- CDON c.*1816C>T Uncertain significance ★★ same type
- CDON c.*2349A>C Uncertain significance ★★ same type
- CDON c.*2377T>C Uncertain significance ★★ same type
- CDON c.*2760A>G Uncertain significance ★★ same type
- CDON p.Ala1099Val Uncertain significance ★★ ⚠ 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/cdon-c-2158-plus-7a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown