Genetic Variant USP9Y:p.Ser2128Ser (chrY-12842411-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004654.4(USP9Y):c.6384C>T(p.Ser2128Ser) 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 0.000062 ( 0 hom., 2 hem., cov: 0)

Exomes 𝑓: 0.00012 ( 0 hom. 44 hem. )

Failed GnomAD Quality Control

Consequence

USP9Y
NM_004654.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0310

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant Y-12842411-C-T is Benign according to our data. Variant chrY-12842411-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661890.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.031 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 2 YL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004654.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP9Y	NM_004654.4	MANE Select	c.6384C>T	p.Ser2128Ser	synonymous	Exon 38 of 46	NP_004645.2	O00507-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
USP9Y	ENST00000338981.7	TSL:1 MANE Select	c.6384C>T	p.Ser2128Ser	synonymous	Exon 38 of 46	ENSP00000342812.3	O00507-1
USP9Y	ENST00000651177.1		c.6384C>T	p.Ser2128Ser	synonymous	Exon 40 of 48	ENSP00000498372.1	O00507-1
USP9Y	ENST00000857541.1		c.6384C>T	p.Ser2128Ser	synonymous	Exon 41 of 49	ENSP00000527600.1

Frequencies

GnomAD3 genomes

AF:

0.0000619

AC:

AN:

32310

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000151

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000443

AC:

AN:

67732

AF XY:

0.0000443

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000948

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000121

AC:

AN:

363082

Hom.:

Cov.:

AF XY:

0.000121

AC XY:

AN XY:

363082

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

7065

American (AMR)

AF:

0.00

AC:

AN:

9490

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6735

East Asian (EAS)

AF:

0.00

AC:

AN:

9474

South Asian (SAS)

AF:

0.00

AC:

AN:

32094

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12872

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1624

European-Non Finnish (NFE)

AF:

0.000145

AC:

AN:

269452

Other (OTH)

AF:

0.000350

AC:

AN:

14276

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000619

AC:

AN:

32310

Hom.:

Cov.:

AF XY:

0.0000619

AC XY:

AN XY:

32310

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8342

American (AMR)

AF:

0.00

AC:

AN:

3455

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

759

East Asian (EAS)

AF:

0.00

AC:

AN:

1267

South Asian (SAS)

AF:

0.00

AC:

AN:

1444

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3039

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000151

AC:

AN:

13278

Other (OTH)

AF:

0.00

AC:

AN:

447

Age Distribution

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.0

(source)

DANN

Benign

0.30

PhyloP100

-0.031

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over