chrY-7367338-G-A

Variant names:

• chrY-7367338-G-A
• rs35195174
• ENST00000528056.5:n.1157-18G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000528056.5(PRKY):​n.1157-18G>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 0.00033 (0 hom., 11 hem., cov: 0)
  • Exomes 𝑓: 0.00025 (0 hom. 75 hem.)
• Consequence: PRKY ENST00000528056.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 1 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Hemizygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKY	NR_028062.1	n.1157-18G>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKY	ENST00000528056.5	n.1157-18G>A		intron_variant	Intron 5 of 7	1
PRKY	ENST00000533551.5	n.816-18G>A		intron_variant	Intron 5 of 6	6
PRKY	ENST00000836332.1	n.634-18G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.000271 AC: 9 AN: 33200 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000827

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000923 AC: 6 AN: 64993 AF XY: 0.0000923

Gnomad AFR exome AF: 0.000337

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000131

Gnomad OTH exome AF: 0.000653

GnomAD4 exome AF: 0.000250 AC: 75 AN: 299526 Hom.: 0 Cov.: 0 AF XY: 0.000250 AC XY: 75 AN XY: 299526

African (AFR) AF: 0.00618 AC: 37 AN: 5987

American (AMR) AF: 0.00 AC: 0 AN: 9325

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6272

East Asian (EAS) AF: 0.00 AC: 0 AN: 9147

South Asian (SAS) AF: 0.0000331 AC: 1 AN: 30199

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12759

Middle Eastern (MID) AF: 0.00208 AC: 3 AN: 1440

European-Non Finnish (NFE) AF: 0.000137 AC: 29 AN: 212237

Other (OTH) AF: 0.000411 AC: 5 AN: 12160

GnomAD4 genome AF: 0.000331 AC: 11 AN: 33266 Hom.: 0 Cov.: 0 AF XY: 0.000331 AC XY: 11 AN XY: 33266

African (AFR) AF: 0.00106 AC: 9 AN: 8520

American (AMR) AF: 0.00 AC: 0 AN: 3516

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 765

East Asian (EAS) AF: 0.00 AC: 0 AN: 1271

South Asian (SAS) AF: 0.00 AC: 0 AN: 1464

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3396

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 72

European-Non Finnish (NFE) AF: 0.000147 AC: 2 AN: 13593

Other (OTH) AF: 0.00 AC: 0 AN: 457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs35195174; hg19: chrY-7235379;