CDON c.640+5G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +5 | donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.91 | donor loss, 5 bp away · masked 0 · deltas |
| Pangolin | Δ0.66 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2, phastCons 1 |
| Non-coding constraint | Z 3.57 | 1 kb window · o/e 0.75 · regional · uncalibrated |
| Overall | ||
| CADD | 20.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDON
- Coding
- c.640+5G>A
- MANE Select
- NM_001378964
- dbSNP
- rs2134676507
- Type
- single nucleotide variant
- Location
- chr11:126018325 (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-640-plus-5g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown