rs73717741

Variant names:

• chr6-4874525-C-G
• rs73717741
• NM_004824.4:c.25-17188C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004824.4(CDYL):​c.25-17188C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 152,272 control chromosomes in the GnomAD database, including 246 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.054 (246 hom., cov: 32)
• Consequence: CDYL NM_004824.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004824.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	NM_004824.4	MANE Select	c.25-17188C>G		intron	N/A	NP_004815.3
	CDYL	NM_001368125.1		c.187-17188C>G		intron	N/A	NP_001355054.1
	CDYL	NM_001368126.1		c.25-17188C>G		intron	N/A	NP_001355055.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	ENST00000397588.8	TSL:1 MANE Select	c.25-17188C>G		intron	N/A	ENSP00000380718.3
	CDYL	ENST00000328908.9	TSL:1	c.187-17188C>G		intron	N/A	ENSP00000330512.5
	CDYL	ENST00000472453.5	TSL:1	n.367-60990C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0544 AC: 8273 AN: 152154 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0543 AC: 8268 AN: 152272 Hom.: 246 Cov.: 32 AF XY: 0.0548 AC XY: 4080 AN XY: 74464

African (AFR) AF: 0.0435 AC: 1809 AN: 41548

American (AMR) AF: 0.0493 AC: 755 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5180

South Asian (SAS) AF: 0.144 AC: 696 AN: 4818

European-Finnish (FIN) AF: 0.0500 AC: 531 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0568 AC: 3864 AN: 68014

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0552 Hom.: 133

Bravo AF: 0.0519

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs73717741; hg19: chr6-4874759;