6-4943770-TAAAAAAAA-TAAAAAAAAAAA

Position:

• chr6-4943770-TAAAAAAAA-TAAAAAAAAAAA

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
• 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 (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: 15795 AN: 144126 Hom.: 960 Cov.: 0

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.0731

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0362

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0911

GnomAD3 exomes AF: 0.0555 AC: 7870 AN: 141918 Hom.: 84 AF XY: 0.0549 AC XY: 4283 AN XY: 77968

Gnomad AFR exome AF: 0.0667

Gnomad AMR exome AF: 0.0276

Gnomad ASJ exome AF: 0.0347

Gnomad EAS exome AF: 0.00945

Gnomad SAS exome AF: 0.0316

Gnomad FIN exome AF: 0.0848

Gnomad NFE exome AF: 0.0685

Gnomad OTH exome AF: 0.0651

GnomAD4 exome AF: 0.0879 AC: 88714 AN: 1009768 Hom.: 485 Cov.: 17 AF XY: 0.0858 AC XY: 43387 AN XY: 505540

Gnomad4 AFR exome AF: 0.0829

Gnomad4 AMR exome AF: 0.0330

Gnomad4 ASJ exome AF: 0.0473

Gnomad4 EAS exome AF: 0.00693

Gnomad4 SAS exome AF: 0.0442

Gnomad4 FIN exome AF: 0.0984

Gnomad4 NFE exome AF: 0.0980

Gnomad4 OTH exome AF: 0.0789

GnomAD4 genome AF: 0.110 AC: 15810 AN: 144160 Hom.: 961 Cov.: 0 AF XY: 0.107 AC XY: 7481 AN XY: 69646

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0680

Gnomad4 ASJ AF: 0.0731

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0932

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;