rs138741332
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001378964.1(CDON):c.2363-31_2363-26del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,566,636 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 25)
Exomes 𝑓: 0.000021 ( 1 hom. )
Consequence
CDON
NM_001378964.1 intron
NM_001378964.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.44
Genes affected
CDON (HGNC:17104): (cell adhesion associated, oncogene regulated) This gene encodes a cell surface receptor that is a member of the immunoglobulin superfamily. The encoded protein contains three fibronectin type III domains and five immunoglobulin-like C2-type domains. This protein is a member of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells and positively regulates myogenesis. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDON | NM_001378964.1 | c.2363-31_2363-26del | intron_variant | ENST00000531738.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDON | ENST00000531738.6 | c.2363-31_2363-26del | intron_variant | 1 | NM_001378964.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151966Hom.: 0 Cov.: 25
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GnomAD3 exomes AF: 0.000154 AC: 38AN: 246792Hom.: 1 AF XY: 0.000134 AC XY: 18AN XY: 133834
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GnomAD4 exome AF: 0.0000212 AC: 30AN: 1414552Hom.: 1 AF XY: 0.0000212 AC XY: 15AN XY: 706698
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152084Hom.: 0 Cov.: 25 AF XY: 0.0000538 AC XY: 4AN XY: 74344
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at