rs9786714

chrY-7305102-A-GchrY-7305102-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_028062.1(PRKY):n.676+997A>G variant causes a intron, non coding transcript 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 NR_028062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Hemizygotes in GnomAd at 8247 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKY	NR_028062.1	n.676+997A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKY	ENST00000528056.5	n.676+997A>G		intron_variant, non_coding_transcript_variant		1
PRKY	ENST00000533551.5	n.335+997A>G		intron_variant, non_coding_transcript_variant

Frequencies

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

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

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.00193

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.219

Alfa AF: 0.111 Hom.: 4628

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786714; hg19: chrY-7173143;