rs34001725

Variant names:

• chrY-7378685-C-T
• rs34001725
• ENST00000528056.5:n.4355C>T

Variant summary

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

The ENST00000528056.5(PRKY):​n.4355C>T variant causes a non coding transcript exon 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 0.060 (0 hom., 2003 hem., cov: 1)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: PRKY ENST00000528056.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 2 publications found

Genes affected

PRKY (HGNC:):

RNU6-941P (HGNC:47904): (RNA, U6 small nuclear 941, pseudogene)

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKY	NR_028062.1	n.4355C>T		non_coding_transcript_exon_variant	Exon 8 of 8
RNU6-941P		n.7378685C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKY	ENST00000528056.5	n.4355C>T		non_coding_transcript_exon_variant	Exon 8 of 8	1
RNU6-941P	ENST00000516346.1	n.14C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 2003 AN: 33072 Hom.: 0 Cov.: 1

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.0478

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0245

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 1

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 3

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0604 AC: 2003 AN: 33136 Hom.: 0 Cov.: 1 AF XY: 0.0604 AC XY: 2003 AN XY: 33136

African (AFR) AF: 0.0380 AC: 323 AN: 8506

American (AMR) AF: 0.0214 AC: 77 AN: 3596

Ashkenazi Jewish (ASJ) AF: 0.0117 AC: 9 AN: 767

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

South Asian (SAS) AF: 0.00 AC: 0 AN: 1492

European-Finnish (FIN) AF: 0.00659 AC: 22 AN: 3337

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

European-Non Finnish (NFE) AF: 0.115 AC: 1551 AN: 13433

Other (OTH) AF: 0.0243 AC: 11 AN: 453

Alfa AF: 0.0497 Hom.: 530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.88
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs34001725; hg19: chrY-7246726;