6-4943770-TAAAAAAAA-TAAAAAAAAAA

Position:

• chr6-4943770-TAAAAAAAA-TAAAAAAAAAA

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
• 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]

ACMG classification

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: 13340 AN: 144264 Hom.: 668 Cov.: 0

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0964

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.0863

GnomAD3 exomes AF: 0.0842 AC: 11951 AN: 141918 Hom.: 56 AF XY: 0.0820 AC XY: 6392 AN XY: 77968

Gnomad AFR exome AF: 0.104

Gnomad AMR exome AF: 0.0537

Gnomad ASJ exome AF: 0.0975

Gnomad EAS exome AF: 0.0706

Gnomad SAS exome AF: 0.0663

Gnomad FIN exome AF: 0.103

Gnomad NFE exome AF: 0.0895

Gnomad OTH exome AF: 0.0961

GnomAD4 exome AF: 0.121 AC: 122684 AN: 1016214 Hom.: 210 Cov.: 17 AF XY: 0.119 AC XY: 60438 AN XY: 508788

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.0635

Gnomad4 ASJ exome AF: 0.119

Gnomad4 EAS exome AF: 0.0841

Gnomad4 SAS exome AF: 0.0913

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.117

GnomAD4 genome AF: 0.0924 AC: 13336 AN: 144292 Hom.: 665 Cov.: 0 AF XY: 0.0923 AC XY: 6435 AN XY: 69710

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0964

Gnomad4 EAS AF: 0.0687

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0972

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.0853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34649909; hg19: chr6-4944004;