chr6-4943770-T-TAAA
Position:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_004824.4(CDYL):c.1332+29_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 0.11 ( 961 hom., cov: 0)
Exomes 𝑓: 0.088 ( 485 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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDYL | NM_004824.4 | c.1332+29_1332+31dup | intron_variant | ENST00000397588.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDYL | ENST00000397588.8 | c.1332+29_1332+31dup | intron_variant | 1 | NM_004824.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.110 AC: 15795AN: 144126Hom.: 960 Cov.: 0
GnomAD3 genomes
AF:
AC:
15795
AN:
144126
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0555 AC: 7870AN: 141918Hom.: 84 AF XY: 0.0549 AC XY: 4283AN XY: 77968
GnomAD3 exomes
AF:
AC:
7870
AN:
141918
Hom.:
AF XY:
AC XY:
4283
AN XY:
77968
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0879 AC: 88714AN: 1009768Hom.: 485 Cov.: 17 AF XY: 0.0858 AC XY: 43387AN XY: 505540
GnomAD4 exome
AF:
AC:
88714
AN:
1009768
Hom.:
Cov.:
17
AF XY:
AC XY:
43387
AN XY:
505540
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.110 AC: 15810AN: 144160Hom.: 961 Cov.: 0 AF XY: 0.107 AC XY: 7481AN XY: 69646
GnomAD4 genome
AF:
AC:
15810
AN:
144160
Hom.:
Cov.:
0
AF XY:
AC XY:
7481
AN XY:
69646
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at