6-4943770-T-TAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_004824.4(CDYL):c.1332+30_1332+31dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.092 ( 665 hom., cov: 0)
Exomes 𝑓: 0.12 ( 210 hom. )
Consequence
CDYL
NM_004824.4 intron
NM_004824.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.378
Genes affected
CDYL (HGNC:1811): (chromodomain Y like) Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDYL | NM_004824.4 | c.1332+30_1332+31dup | intron_variant | ENST00000397588.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDYL | ENST00000397588.8 | c.1332+30_1332+31dup | intron_variant | 1 | NM_004824.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0925 AC: 13340AN: 144264Hom.: 668 Cov.: 0
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GnomAD3 exomes AF: 0.0842 AC: 11951AN: 141918Hom.: 56 AF XY: 0.0820 AC XY: 6392AN XY: 77968
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GnomAD4 exome AF: 0.121 AC: 122684AN: 1016214Hom.: 210 Cov.: 17 AF XY: 0.119 AC XY: 60438AN XY: 508788
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GnomAD4 genome AF: 0.0924 AC: 13336AN: 144292Hom.: 665 Cov.: 0 AF XY: 0.0923 AC XY: 6435AN XY: 69710
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at