chrY-7303916-G-A

Variant names:

• chrY-7303916-G-A
• rs35147341
• ENST00000528056.5:n.508-21G>A

Variant summary

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

The ENST00000528056.5(PRKY):​n.508-21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 ENST00000528056.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 2 publications found

Genes affected

PRKY (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528056.5. 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
	PRKY	NR_028062.1		n.508-21G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKY	ENST00000528056.5	TSL:1	n.508-21G>A		intron	N/A
	PRKY	ENST00000533551.5	TSL:6	n.167-21G>A		intron	N/A
	PRKY	ENST00000836332.1		n.105-21G>A		intron	N/A

Frequencies

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

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

GnomAD2 exomes AF: 0.0247 AC: 1666 AN: 67382 AF XY: 0.0247

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 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

African (AFR) AF: 0.000710 AC: 5 AN: 7039

American (AMR) AF: 0.000526 AC: 5 AN: 9507

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6709

East Asian (EAS) AF: 0.000106 AC: 1 AN: 9468

South Asian (SAS) AF: 0.136 AC: 4326 AN: 31712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12876

Middle Eastern (MID) AF: 0.00450 AC: 7 AN: 1557

European-Non Finnish (NFE) AF: 0.000711 AC: 190 AN: 267169

Other (OTH) AF: 0.0136 AC: 192 AN: 14164

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

African (AFR) AF: 0.000344 AC: 3 AN: 8731

American (AMR) AF: 0.000265 AC: 1 AN: 3776

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 782

East Asian (EAS) AF: 0.00 AC: 0 AN: 1261

South Asian (SAS) AF: 0.146 AC: 222 AN: 1520

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3539

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.000293 AC: 4 AN: 13642

Other (OTH) AF: 0.00216 AC: 1 AN: 464

Alfa AF: 0.00336 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.0060
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs35147341; hg19: chrY-7171957;