Genetic Variant USP9X:c.3149-8dupT (chrX-41183983-C-CT) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001039591.3(USP9X):c.3149-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00841 in 1,192,392 control chromosomes in the GnomAD database, including 37 homozygotes. There are 3,131 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0058 ( 1 hom., 159 hem., cov: 22)

Exomes 𝑓: 0.0087 ( 36 hom. 2972 hem. )

Consequence

USP9X
NM_001039591.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.165

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]

USP9X links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-41183983-C-CT is Benign according to our data. Variant chrX-41183983-C-CT is described in ClinVar as [Benign]. Clinvar id is 445459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00585 (652/111479) while in subpopulation NFE AF= 0.0101 (533/53007). AF 95% confidence interval is 0.00935. There are 1 homozygotes in gnomad4. There are 159 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 159 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP9X	NM_001039591.3 link	c.3149-8dupT		splice_region_variant, intron_variant	Intron 21 of 44	ENST00000378308.7	NP_001034680.2	Q93008-1Q86X58Q6P468

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP9X	ENST00000378308.7 link	c.3149-15_3149-14insT		intron_variant	Intron 21 of 44	5	NM_001039591.3	ENSP00000367558.2		Q93008-1

Frequencies

GnomAD3 genomes

AF:

0.00585

AC:

652

AN:

111426

Hom.:

Cov.:

AF XY:

0.00473

AC XY:

159

AN XY:

33622

show subpopulations

Gnomad AFR

AF:

0.00131

Gnomad AMI

AF:

0.00147

Gnomad AMR

AF:

0.00181

Gnomad ASJ

AF:

0.00492

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00112

Gnomad FIN

AF:

0.00623

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.00331

GnomAD3 exomes

AF:

0.00586

AC:

941

AN:

160631

Hom.:

AF XY:

0.00571

AC XY:

297

AN XY:

51969

show subpopulations

Gnomad AFR exome

AF:

0.00110

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.00342

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00170

Gnomad FIN exome

AF:

0.00695

Gnomad NFE exome

AF:

0.00976

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.00868

AC:

9377

AN:

1080913

Hom.:

Cov.:

AF XY:

0.00847

AC XY:

2972

AN XY:

350919

show subpopulations

Gnomad4 AFR exome

AF:

0.00106

Gnomad4 AMR exome

AF:

0.00101

Gnomad4 ASJ exome

AF:

0.00448

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00183

Gnomad4 FIN exome

AF:

0.00750

Gnomad4 NFE exome

AF:

0.0102

Gnomad4 OTH exome

AF:

0.00668

GnomAD4 genome

AF:

0.00585

AC:

652

AN:

111479

Hom.:

Cov.:

AF XY:

0.00472

AC XY:

159

AN XY:

33685

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00181

Gnomad4 ASJ

AF:

0.00492

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00112

Gnomad4 FIN

AF:

0.00623

Gnomad4 NFE

AF:

0.0101

Gnomad4 OTH

AF:

0.00327

Alfa

AF:

0.00716

Hom.:

Bravo

AF:

0.00513

Asia WGS

AF:

0.000399

AC:

AN:

2519

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Apr 08, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 18, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

X-41183983-CTT-CTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over