Genetic Variant USP9Y:p.Arg419His (chrY-12738248-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_004654.4(USP9Y):c.1256G>A(p.Arg419His) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000030 ( 0 hom., 1 hem., cov: 0)

Exomes 𝑓: 0.0000083 ( 0 hom. 3 hem. )

Failed GnomAD Quality Control

Consequence

USP9Y
NM_004654.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.32

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP9Y	NM_004654.4 link	c.1256G>A	p.Arg419His	missense_variant	Exon 11 of 46	ENST00000338981.7	NP_004645.2	O00507-1
USP9Y	XM_047442772.1 link	c.1256G>A	p.Arg419His	missense_variant	Exon 11 of 46		XP_047298728.1
USP9Y	XM_047442771.1 link	c.1022G>A	p.Arg341His	missense_variant	Exon 10 of 45		XP_047298727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
USP9Y	ENST00000338981.7 link	c.1256G>A	p.Arg419His	missense_variant	Exon 11 of 46	1	NM_004654.4	ENSP00000342812.3	O00507-1
USP9Y	ENST00000651177.1 link	c.1256G>A	p.Arg419His	missense_variant	Exon 13 of 48			ENSP00000498372.1	O00507-1
USP9Y	ENST00000426564.6 link	n.1268G>A		non_coding_transcript_exon_variant	Exon 9 of 44	2

Frequencies

GnomAD3 genomes

AF:

0.0000301

AC:

AN:

33245

Hom.:

Cov.:

AF XY:

0.0000301

AC XY:

AN XY:

33245

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:

0.0000742

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000830

AC:

AN:

361637

Hom.:

Cov.:

AF XY:

0.00000830

AC XY:

AN XY:

361637

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000315

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000744

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000301

AC:

AN:

33245

Hom.:

Cov.:

AF XY:

0.0000301

AC XY:

AN XY:

33245

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000742

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Spermatogenic failure, Y-linked, 2

Uncertain:1

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.61

BayesDel_addAF

Uncertain

0.062

BayesDel_noAF

Benign

-0.15

CADD

Uncertain

DANN

Uncertain

0.98

DEOGEN2

Benign

0.26

FATHMM_MKL

Uncertain

0.95

LIST_S2

Pathogenic

0.98

M_CAP

Uncertain

0.26

MetaRNN

Uncertain

0.50

MutationAssessor

Uncertain

2.7

PROVEAN

Pathogenic

-4.4

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.11

Vest4

0.60

MVP

0.59

MPC

0.030

GERP RS

2.3

Varity_R

0.48

gMVP

0.65

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over