rs9785813

Variant names:

• chrY-7295440-C-T
• rs9785813
• ENST00000528056.5:n.508-8497C>T

Variant summary

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

The ENST00000528056.5(PRKY):​n.508-8497C>T 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 0.15 (0 hom., 4979 hem., cov: 0)
• Consequence: PRKY ENST00000528056.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKY	NR_028062.1		n.508-8497C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKY	ENST00000528056.5	TSL:1	n.508-8497C>T		intron	N/A
	PRKY	ENST00000533551.5	TSL:6	n.167-8497C>T		intron	N/A
	PRKY	ENST00000836332.1		n.105-8497C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 4946 AN: 32624 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00202

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0141

Gnomad NFE AF: 0.00207

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.152 AC: 4979 AN: 32686 Hom.: 0 Cov.: 0 AF XY: 0.152 AC XY: 4979 AN XY: 32686

African (AFR) AF: 0.593 AC: 4779 AN: 8058

American (AMR) AF: 0.0373 AC: 130 AN: 3489

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 767

East Asian (EAS) AF: 0.00 AC: 0 AN: 1241

South Asian (SAS) AF: 0.00202 AC: 3 AN: 1488

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3380

Middle Eastern (MID) AF: 0.0143 AC: 1 AN: 70

European-Non Finnish (NFE) AF: 0.00207 AC: 28 AN: 13518

Other (OTH) AF: 0.0832 AC: 38 AN: 457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9785813;

hg19: chrY-7163481;