Y-12842411-C-T

Variant summary

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

The NM_004654.4(USP9Y):​c.6384C>T​(p.Ser2128=) 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

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0310
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]

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=-0.54).
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 id 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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
USP9YNM_004654.4 linkuse as main transcriptc.6384C>T p.Ser2128= synonymous_variant 38/46 ENST00000338981.7
USP9YXM_047442772.1 linkuse as main transcriptc.6384C>T p.Ser2128= synonymous_variant 38/46
USP9YXM_047442771.1 linkuse as main transcriptc.6150C>T p.Ser2050= synonymous_variant 37/45

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
USP9YENST00000338981.7 linkuse as main transcriptc.6384C>T p.Ser2128= synonymous_variant 38/461 NM_004654.4 P1O00507-1
USP9YENST00000651177.1 linkuse as main transcriptc.6384C>T p.Ser2128= synonymous_variant 40/48 P1O00507-1
USP9YENST00000426564.6 linkuse as main transcriptn.6411C>T non_coding_transcript_exon_variant 36/442

Frequencies

GnomAD3 genomes
AF:
0.0000619
AC:
2
AN:
32310
Hom.:
0
Cov.:
0
AF XY:
0.0000619
AC XY:
2
AN XY:
32310
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
GnomAD3 exomes
AF:
0.0000443
AC:
3
AN:
67732
Hom.:
0
AF XY:
0.0000443
AC XY:
3
AN XY:
67732
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 SAS 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:
44
AN:
363082
Hom.:
0
Cov.:
0
AF XY:
0.000121
AC XY:
44
AN XY:
363082
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000145
Gnomad4 OTH exome
AF:
0.000350
GnomAD4 genome
AF:
0.0000619
AC:
2
AN:
32310
Hom.:
0
Cov.:
0
AF XY:
0.0000619
AC XY:
2
AN XY:
32310
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:
0.000151
Gnomad4 OTH
AF:
0.00

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2023USP9Y: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
8.0
DANN
Benign
0.30

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

LitVar

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

Other links and lift over

dbSNP: rs200311491; hg19: chrY-14954337; COSMIC: COSV59099539; COSMIC: COSV59099539; API