6-4928153-A-G

Variant names:

• chr6-4928153-A-G
• rs1112267
• NM_004824.4:c.692-7362A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004824.4(CDYL):​c.692-7362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,274 control chromosomes in the GnomAD database, including 61,147 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 0.89 (61147 hom., cov: 33)
• Consequence: CDYL NM_004824.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL	NM_004824.4	c.692-7362A>G		intron_variant	Intron 2 of 6	ENST00000397588.8	NP_004815.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL	ENST00000397588.8	c.692-7362A>G		intron_variant	Intron 2 of 6	1	NM_004824.4	ENSP00000380718.3

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135936 AN: 152156 Hom.: 61110 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.893 AC: 136026 AN: 152274 Hom.: 61147 Cov.: 33 AF XY: 0.891 AC XY: 66369 AN XY: 74466

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.909

Alfa AF: 0.944 Hom.: 15936

Bravo AF: 0.883

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs1112267; hg19: chr6-4928387;