rs34442126

Variant names:

• chrY-12810648-T-C
• rs34442126
• NM_004654.4:c.4093-24T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004654.4(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 NM_004654.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 8 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=-0.86).
• 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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 2718 YL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP9Y	NM_004654.4	c.4093-24T>C		intron_variant	Intron 28 of 45	ENST00000338981.7	NP_004645.2
USP9Y	XM_047442772.1	c.4093-24T>C		intron_variant	Intron 28 of 45		XP_047298728.1
USP9Y	XM_047442771.1	c.3859-24T>C		intron_variant	Intron 27 of 44		XP_047298727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP9Y	ENST00000338981.7	c.4093-24T>C		intron_variant	Intron 28 of 45	1	NM_004654.4	ENSP00000342812.3
USP9Y	ENST00000651177.1	c.4093-24T>C		intron_variant	Intron 30 of 47			ENSP00000498372.1
USP9Y	ENST00000426564.6	n.4105-24T>C		intron_variant	Intron 26 of 43	2

Frequencies

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

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

GnomAD2 exomes AF: 0.0698 AC: 4007 AN: 57377 AF XY: 0.0698

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 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

African (AFR) AF: 0.000143 AC: 1 AN: 6972

American (AMR) AF: 0.00141 AC: 13 AN: 9237

Ashkenazi Jewish (ASJ) AF: 0.000151 AC: 1 AN: 6628

East Asian (EAS) AF: 0.00448 AC: 42 AN: 9381

South Asian (SAS) AF: 0.000127 AC: 4 AN: 31397

European-Finnish (FIN) AF: 0.660 AC: 8321 AN: 12612

Middle Eastern (MID) AF: 0.00146 AC: 2 AN: 1367

European-Non Finnish (NFE) AF: 0.00851 AC: 2248 AN: 264031

Other (OTH) AF: 0.0264 AC: 369 AN: 13991

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

African (AFR) AF: 0.000348 AC: 3 AN: 8620

American (AMR) AF: 0.000548 AC: 2 AN: 3650

Ashkenazi Jewish (ASJ) AF: 0.00130 AC: 1 AN: 770

East Asian (EAS) AF: 0.0148 AC: 19 AN: 1287

South Asian (SAS) AF: 0.00 AC: 0 AN: 1505

European-Finnish (FIN) AF: 0.756 AC: 2266 AN: 2998

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 73

European-Non Finnish (NFE) AF: 0.0308 AC: 413 AN: 13403

Other (OTH) AF: 0.0300 AC: 14 AN: 466

Alfa AF: 0.0339 Hom.: 1095

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
PhyloP100		0.086

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: rs34442126; hg19: chrY-14922583;