rs9786714

Variant names:

• chrY-7305102-A-G
• rs9786714
• ENST00000528056.5:n.676+997A>G

Your query was ambiguous. Multiple possible variants found:

• chrY-7305102-A-G
• chrY-7305102-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000528056.5(PRKY):​n.676+997A>G 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 0.27 (0 hom., 8301 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: PRKY ENST00000528056.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKY	NR_028062.1	n.676+997A>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKY	ENST00000528056.5	n.676+997A>G		intron_variant	Intron 2 of 7	1
PRKY	ENST00000533551.5	n.335+997A>G		intron_variant	Intron 2 of 6	6
PRKY	ENST00000836332.1	n.273+997A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.270 AC: 8247 AN: 30510 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.00193

Gnomad MID AF: 0.492

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.220

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.272 AC: 8301 AN: 30573 Hom.: 0 Cov.: 0 AF XY: 0.272 AC XY: 8301 AN XY: 30573

African (AFR) AF: 0.735 AC: 5669 AN: 7709

American (AMR) AF: 0.207 AC: 680 AN: 3280

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 238 AN: 730

East Asian (EAS) AF: 0.124 AC: 143 AN: 1149

South Asian (SAS) AF: 0.263 AC: 337 AN: 1279

European-Finnish (FIN) AF: 0.00193 AC: 6 AN: 3106

Middle Eastern (MID) AF: 0.500 AC: 31 AN: 62

European-Non Finnish (NFE) AF: 0.0851 AC: 1074 AN: 12622

Other (OTH) AF: 0.219 AC: 95 AN: 434

Alfa AF: 0.177 Hom.: 9937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.13
PhyloP100		-2.2
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: rs9786714; hg19: chrY-7173143;