rs2032604

Positions:

• chrY-12857709-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004654.4(USP9Y):​c.7530+48T>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 0.035 (0 hom., 1162 hem., cov: 0)
  • Exomes 𝑓: 0.055 (0 hom. 12696 hem.)
• Consequence: USP9Y NM_004654.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

USP9Y (HGNC:12633): (ubiquitin specific peptidase 9 Y-linked) This gene is a member of the peptidase C19 family. It encodes a protein that is similar to ubiquitin-specific proteases, which cleave the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP9Y	NM_004654.4	c.7530+48T>G		intron_variant		ENST00000338981.7
USP9Y	XM_047442771.1	c.7296+48T>G		intron_variant
USP9Y	XM_047442772.1	c.7530+48T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9Y	ENST00000338981.7	c.7530+48T>G		intron_variant		1	NM_004654.4	P1

Frequencies

GnomAD3 genomes AF: 0.0348 AC: 1163 AN: 33437 Hom.: 0 Cov.: 0 AF XY: 0.0348 AC XY: 1163 AN XY: 33437

Gnomad AFR AF: 0.00833

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.000767

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.000294

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0817

GnomAD3 exomes AF: 0.0666 AC: 2568 AN: 38542 Hom.: 0 AF XY: 0.0666 AC XY: 2568 AN XY: 38542

Gnomad AFR exome AF: 0.00895

Gnomad AMR exome AF: 0.0590

Gnomad ASJ exome AF: 0.186

Gnomad EAS exome AF: 0.000741

Gnomad SAS exome AF: 0.148

Gnomad FIN exome AF: 0.000820

Gnomad NFE exome AF: 0.0444

Gnomad OTH exome AF: 0.0743

GnomAD4 exome AF: 0.0550 AC: 12696 AN: 230744 Hom.: 0 Cov.: 0 AF XY: 0.0550 AC XY: 12696 AN XY: 230744

Gnomad4 AFR exome AF: 0.0109

Gnomad4 AMR exome AF: 0.0637

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.000497

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.00142

Gnomad4 NFE exome AF: 0.0383

Gnomad4 OTH exome AF: 0.0781

GnomAD4 genome AF: 0.0347 AC: 1162 AN: 33496 Hom.: 0 Cov.: 0 AF XY: 0.0347 AC XY: 1162 AN XY: 33496

Gnomad4 AFR AF: 0.00828

Gnomad4 AMR AF: 0.0499

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.000768

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.000294

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0653 Hom.: 2533

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.035
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032604; hg19: chrY-14969634;