rs34001725

Positions:

• chrY-7378685-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

PRKY (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PRKY	NR_028062.1	n.4355C>T		non_coding_transcript_exon_variant	8/8
RNU6-941P		n.7378685C>T		intragenic_variant

Ensembl

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

Frequencies

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

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

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0117

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34001725; hg19: chrY-7246726;