dbSNP rs1286380745: USP9Y:p.Gly2115Arg (chrY-12842370-G-C) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_004654.4(USP9Y):c.6343G>C(p.Gly2115Arg) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G2115C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.000022 ( 0 hom. 8 hem. )

Failed GnomAD Quality Control

Consequence

USP9Y
NM_004654.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 9.43

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: Uncertain_significance. The variant received 1 ACMG points.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.791

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.6343G>C	p.Gly2115Arg	missense	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.6343G>C	p.Gly2115Arg	missense	Exon 38 of 46	ENSP00000342812.3	O00507-1
USP9Y	ENST00000651177.1		c.6343G>C	p.Gly2115Arg	missense	Exon 40 of 48	ENSP00000498372.1	O00507-1
USP9Y	ENST00000857541.1		c.6343G>C	p.Gly2115Arg	missense	Exon 41 of 49	ENSP00000527600.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000148

AC:

AN:

67789

AF XY:

0.0000148

show subpopulations

Gnomad AFR exome

AF:

0.000324

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000220

AC:

AN:

363000

Hom.:

Cov.:

AF XY:

0.0000220

AC XY:

AN XY:

363000

show subpopulations

African (AFR)

AF:

0.000283

AC:

AN:

7064

American (AMR)

AF:

0.00

AC:

AN:

9492

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6739

East Asian (EAS)

AF:

0.00

AC:

AN:

9479

South Asian (SAS)

AF:

0.00

AC:

AN:

32093

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12879

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1609

European-Non Finnish (NFE)

AF:

0.0000223

AC:

AN:

269379

Other (OTH)

AF:

0.00

AC:

AN:

14266

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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.50

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

(source)

DANN

Benign

0.77

DEOGEN2

Benign

0.0052

FATHMM_MKL

Uncertain

0.96

LIST_S2

Pathogenic

0.99

M_CAP

Uncertain

0.24

MetaRNN

Pathogenic

0.79

MutationAssessor

Benign

1.6

PhyloP100

9.4

PROVEAN

Benign

-1.0

Sift

Benign

0.087

Sift4G

Benign

0.19

Polyphen

0.57

Vest4

0.80

MVP

0.78

MPC

0.0088

GERP RS

2.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.30

gMVP

0.66

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

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over