Genetic Variant USP9Y:c.7530+48T>G (chrY-12857709-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

14 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

new If you want to explore the variant's impact on the transcript NM_004654.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

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.7530+48T>G		intron	N/A	NP_004645.2	O00507-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
USP9Y	ENST00000338981.7	TSL:1 MANE Select	c.7530+48T>G	intron	N/A	ENSP00000342812.3	O00507-1
USP9Y	ENST00000651177.1		c.7530+48T>G	intron	N/A	ENSP00000498372.1	O00507-1
USP9Y	ENST00000857541.1		c.7530+48T>G	intron	N/A	ENSP00000527600.1

Frequencies

GnomAD3 genomes

AF:

0.0348

AC:

1163

AN:

33437

Hom.:

Cov.:

show subpopulations

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

show subpopulations

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.:

Cov.:

AF XY:

0.0550

AC XY:

12696

AN XY:

230744

show subpopulations

African (AFR)

AF:

0.0109

AC:

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:

AN:

8055

South Asian (SAS)

AF:

0.155

AC:

4086

AN:

26290

European-Finnish (FIN)

AF:

0.00142

AC:

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

Age Distribution

Exome Hom

Variant carriers

172

344

516

688

860

<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:

0.0347

AC:

1162

AN:

33496

Hom.:

Cov.:

AF XY:

0.0347

AC XY:

1162

AN XY:

33496

show subpopulations

African (AFR)

AF:

0.00828

AC:

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:

AN:

1302

South Asian (SAS)

AF:

0.116

AC:

173

AN:

1487

European-Finnish (FIN)

AF:

0.000294

AC:

AN:

3397

Middle Eastern (MID)

AF:

0.110

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0391

AC:

531

AN:

13567

Other (OTH)

AF:

0.0833

AC:

AN:

468

Age Distribution

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0878

Hom.:

3776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.035

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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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