rs10463

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001039591.3(USP9X):​c.*164A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0816 in 636,648 control chromosomes in the GnomAD database, including 1,707 homozygotes. There are 13,354 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 216 hom., 1898 hem., cov: 23)
Exomes 𝑓: 0.086 ( 1491 hom. 11456 hem. )

Consequence

USP9X
NM_001039591.3 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.34
Variant links:
Genes affected
USP9X (HGNC:12632): (ubiquitin specific peptidase 9 X-linked) This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation. Mutations in this gene have been associated with Turner syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant X-41232688-A-G is Benign according to our data. Variant chrX-41232688-A-G is described in ClinVar as [Benign]. Clinvar id is 1296676.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0904 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
USP9XNM_001039591.3 linkuse as main transcriptc.*164A>G 3_prime_UTR_variant 45/45 ENST00000378308.7 NP_001034680.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
USP9XENST00000378308.7 linkuse as main transcriptc.*164A>G 3_prime_UTR_variant 45/455 NM_001039591.3 ENSP00000367558 P4Q93008-1

Frequencies

GnomAD3 genomes
AF:
0.0603
AC:
6755
AN:
111941
Hom.:
216
Cov.:
23
AF XY:
0.0556
AC XY:
1897
AN XY:
34117
show subpopulations
Gnomad AFR
AF:
0.0124
Gnomad AMI
AF:
0.161
Gnomad AMR
AF:
0.0440
Gnomad ASJ
AF:
0.122
Gnomad EAS
AF:
0.000550
Gnomad SAS
AF:
0.0427
Gnomad FIN
AF:
0.0561
Gnomad MID
AF:
0.118
Gnomad NFE
AF:
0.0925
Gnomad OTH
AF:
0.0539
GnomAD4 exome
AF:
0.0862
AC:
45220
AN:
524658
Hom.:
1491
Cov.:
8
AF XY:
0.0992
AC XY:
11456
AN XY:
115458
show subpopulations
Gnomad4 AFR exome
AF:
0.0126
Gnomad4 AMR exome
AF:
0.0382
Gnomad4 ASJ exome
AF:
0.113
Gnomad4 EAS exome
AF:
0.000129
Gnomad4 SAS exome
AF:
0.0696
Gnomad4 FIN exome
AF:
0.0644
Gnomad4 NFE exome
AF:
0.0982
Gnomad4 OTH exome
AF:
0.0777
GnomAD4 genome
AF:
0.0603
AC:
6755
AN:
111990
Hom.:
216
Cov.:
23
AF XY:
0.0555
AC XY:
1898
AN XY:
34176
show subpopulations
Gnomad4 AFR
AF:
0.0124
Gnomad4 AMR
AF:
0.0440
Gnomad4 ASJ
AF:
0.122
Gnomad4 EAS
AF:
0.000552
Gnomad4 SAS
AF:
0.0439
Gnomad4 FIN
AF:
0.0561
Gnomad4 NFE
AF:
0.0925
Gnomad4 OTH
AF:
0.0526
Alfa
AF:
0.0799
Hom.:
2981
Bravo
AF:
0.0557

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxSep 04, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.36
CADD
Benign
12
DANN
Benign
0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

LitVar

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

Other links and lift over

dbSNP: rs10463; hg19: chrX-41091941; API