Variant chrY-12778040-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004654.4(USP9Y):c.2661C>T(p.Leu887=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., 50 hem., cov: 0)

Exomes 𝑓: 0.0018 ( 0 hom. 664 hem. )

Consequence

USP9Y
NM_004654.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.439

Variant links:

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]

USP9Y links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant Y-12778040-C-T is Benign according to our data. Variant chrY-12778040-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661886.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.439 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 50 YL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
USP9Y	NM_004654.4 linkuse as main transcript	c.2661C>T	p.Leu887=	synonymous_variant	20/46	ENST00000338981.7
USP9Y	XM_047442772.1 linkuse as main transcript	c.2661C>T	p.Leu887=	synonymous_variant	20/46
USP9Y	XM_047442771.1 linkuse as main transcript	c.2427C>T	p.Leu809=	synonymous_variant	19/45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9Y	ENST00000338981.7 linkuse as main transcript	c.2661C>T	p.Leu887=	synonymous_variant	20/46	1	NM_004654.4	P1	O00507-1
USP9Y	ENST00000651177.1 linkuse as main transcript	c.2661C>T	p.Leu887=	synonymous_variant	22/48			P1	O00507-1
USP9Y	ENST00000426564.6 linkuse as main transcript	n.2673C>T		non_coding_transcript_exon_variant	18/44	2

Frequencies

GnomAD3 genomes

AF:

0.00151

AC:

AN:

32461

Hom.:

Cov.:

AF XY:

0.00151

AC XY:

AN XY:

32461

show subpopulations

Gnomad AFR

AF:

0.000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000574

Gnomad ASJ

AF:

0.0302

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00141

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00128

Gnomad OTH

AF:

0.00708

GnomAD3 exomes

AF:

0.00334

AC:

217

AN:

64901

Hom.:

AF XY:

0.00334

AC XY:

217

AN XY:

64901

show subpopulations

Gnomad AFR exome

AF:

0.000336

Gnomad AMR exome

AF:

0.00144

Gnomad ASJ exome

AF:

0.0523

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00191

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00156

Gnomad OTH exome

AF:

0.00392

GnomAD4 exome

AF:

0.00184

AC:

664

AN:

360895

Hom.:

Cov.:

AF XY:

0.00184

AC XY:

664

AN XY:

360895

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00191

Gnomad4 ASJ exome

AF:

0.0447

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00247

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000638

Gnomad4 OTH exome

AF:

0.00599

GnomAD4 genome

AF:

0.00154

AC:

AN:

32522

Hom.:

Cov.:

AF XY:

0.00154

AC XY:

AN XY:

32522

show subpopulations

Gnomad4 AFR

AF:

0.000240

Gnomad4 AMR

AF:

0.000573

Gnomad4 ASJ

AF:

0.0302

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00211

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00128

Gnomad4 OTH

AF:

0.00703

Alfa

AF:

0.00872

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2022

USP9Y: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

2.6

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over