rs35147341

chrY-7303916-G-A

Variant summary

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

The NR_028062.1(PRKY):n.508-21G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 394,200 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0068 (0 hom., 231 hem., cov: 0)
  • Exomes 𝑓: 0.013 (0 hom. 4726 hem.)
• Consequence: PRKY NR_028062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

PRKY (HGNC:9444): (protein kinase Y-linked (pseudogene)) This gene is similar to the protein kinase, X-linked gene in the pseudoautosomal region of the X chromosome. The gene is classified as a transcribed pseudogene because it has lost a coding exon that results in all transcripts being candidates for nonsense-mediated decay (NMD) and unlikely to express a protein. Abnormal recombination between this gene and a related gene on chromosome X is a frequent cause of XX males and XY females. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKY	NR_028062.1	n.508-21G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKY	ENST00000528056.5	n.508-21G>A		intron_variant, non_coding_transcript_variant		1
PRKY	ENST00000533551.5	n.167-21G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00672 AC: 228 AN: 33938 Hom.: 0 Cov.: 0 AF XY: 0.00672 AC XY: 228 AN XY: 33938

Gnomad AFR AF: 0.000346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000265

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000293

Gnomad OTH AF: 0.00217

GnomAD3 exomes AF: 0.0247 AC: 1666 AN: 67382 Hom.: 0 AF XY: 0.0247 AC XY: 1666 AN XY: 67382

Gnomad AFR exome AF: 0.000970

Gnomad AMR exome AF: 0.000560

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000221

Gnomad SAS exome AF: 0.141

Gnomad FIN exome AF: 0.000178

Gnomad NFE exome AF: 0.000986

Gnomad OTH exome AF: 0.0126

GnomAD4 exome AF: 0.0131 AC: 4726 AN: 360201 Hom.: 0 Cov.: 5 AF XY: 0.0131 AC XY: 4726 AN XY: 360201

Gnomad4 AFR exome AF: 0.000710

Gnomad4 AMR exome AF: 0.000526

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000106

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000711

Gnomad4 OTH exome AF: 0.0136

GnomAD4 genome AF: 0.00679 AC: 231 AN: 33999 Hom.: 0 Cov.: 0 AF XY: 0.00679 AC XY: 231 AN XY: 33999

Gnomad4 AFR AF: 0.000344

Gnomad4 AMR AF: 0.000265

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000293

Gnomad4 OTH AF: 0.00216

Alfa AF: 0.00336 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	4.9
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35147341; hg19: chrY-7171957;