rs34442126

Positions:

• chrY-12810648-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000338981.7(USP9Y):​c.4093-24T>C 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 0.082 (0 hom., 2718 hem., cov: 0)
  • Exomes 𝑓: 0.031 (0 hom. 11001 hem.)
• Consequence: USP9Y ENST00000338981.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0824 (2718/32986) while in subpopulation NFE AF= 0.0308 (413/13403). AF 95% confidence interval is 0.0284. There are 0 homozygotes in gnomad4. There are 2718 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd4 at 2718 YL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP9Y	NM_004654.4	c.4093-24T>C		intron_variant		ENST00000338981.7	NP_004645.2
USP9Y	XM_047442771.1	c.3859-24T>C		intron_variant			XP_047298727.1
USP9Y	XM_047442772.1	c.4093-24T>C		intron_variant			XP_047298728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000338981.7	c.4093-24T>C		intron_variant		1	NM_004654.4	ENSP00000342812	P1
USP9Y	ENST00000651177.1	c.4093-24T>C		intron_variant				ENSP00000498372	P1
USP9Y	ENST00000426564.6	n.4105-24T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 2717 AN: 32924 Hom.: 0 Cov.: 0 AF XY: 0.0825 AC XY: 2717 AN XY: 32924

Gnomad AFR AF: 0.000350

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000549

Gnomad ASJ AF: 0.00130

Gnomad EAS AF: 0.0140

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0303

GnomAD3 exomes AF: 0.0698 AC: 4007 AN: 57377 Hom.: 0 AF XY: 0.0698 AC XY: 4007 AN XY: 57377

Gnomad AFR exome AF: 0.000753

Gnomad AMR exome AF: 0.00108

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00594

Gnomad SAS exome AF: 0.000197

Gnomad FIN exome AF: 0.699

Gnomad NFE exome AF: 0.0163

Gnomad OTH exome AF: 0.0524

GnomAD4 exome AF: 0.0309 AC: 11001 AN: 355616 Hom.: 0 Cov.: 0 AF XY: 0.0309 AC XY: 11001 AN XY: 355616

Gnomad4 AFR exome AF: 0.000143

Gnomad4 AMR exome AF: 0.00141

Gnomad4 ASJ exome AF: 0.000151

Gnomad4 EAS exome AF: 0.00448

Gnomad4 SAS exome AF: 0.000127

Gnomad4 FIN exome AF: 0.660

Gnomad4 NFE exome AF: 0.00851

Gnomad4 OTH exome AF: 0.0264

GnomAD4 genome AF: 0.0824 AC: 2718 AN: 32986 Hom.: 0 Cov.: 0 AF XY: 0.0824 AC XY: 2718 AN XY: 32986

Gnomad4 AFR AF: 0.000348

Gnomad4 AMR AF: 0.000548

Gnomad4 ASJ AF: 0.00130

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.0308

Gnomad4 OTH AF: 0.0300

Alfa AF: 0.0242 Hom.: 312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.59
DANN	Benign	0.55

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: rs34442126; hg19: chrY-14922583;