chrY-12857709-T-G

Variant names:

• chrY-12857709-T-G
• rs2032604
• NM_004654.4:c.7530+48T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
USP9Y	NM_004654.4	c.7530+48T>G		intron_variant	Intron 45 of 45	ENST00000338981.7	NP_004645.2
USP9Y	XM_047442772.1	c.7530+48T>G		intron_variant	Intron 45 of 45		XP_047298728.1
USP9Y	XM_047442771.1	c.7296+48T>G		intron_variant	Intron 44 of 44		XP_047298727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000338981.7	c.7530+48T>G		intron_variant	Intron 45 of 45	1	NM_004654.4	ENSP00000342812.3

Frequencies

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

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

GnomAD2 exomes AF: 0.0666 AC: 2568 AN: 38542 AF XY: 0.0666

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 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

African (AFR) AF: 0.0109 AC: 51 AN: 4694

American (AMR) AF: 0.0637 AC: 472 AN: 7413

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 1097 AN: 5725

East Asian (EAS) AF: 0.000497 AC: 4 AN: 8055

South Asian (SAS) AF: 0.155 AC: 4086 AN: 26290

European-Finnish (FIN) AF: 0.00142 AC: 16 AN: 11266

Middle Eastern (MID) AF: 0.167 AC: 222 AN: 1332

European-Non Finnish (NFE) AF: 0.0383 AC: 5968 AN: 155985

Other (OTH) AF: 0.0781 AC: 780 AN: 9984

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

African (AFR) AF: 0.00828 AC: 71 AN: 8572

American (AMR) AF: 0.0499 AC: 182 AN: 3650

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 137 AN: 761

East Asian (EAS) AF: 0.000768 AC: 1 AN: 1302

South Asian (SAS) AF: 0.116 AC: 173 AN: 1487

European-Finnish (FIN) AF: 0.000294 AC: 1 AN: 3397

Middle Eastern (MID) AF: 0.110 AC: 8 AN: 73

European-Non Finnish (NFE) AF: 0.0391 AC: 531 AN: 13567

Other (OTH) AF: 0.0833 AC: 39 AN: 468

Alfa AF: 0.0878 Hom.: 3776

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
PhyloP100		-1.2

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

Other links and lift over

dbSNP: rs2032604; hg19: chrY-14969634;