X-41123184-G-A

Position:

• chrX-41123184-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001039591.3(USP9X):​c.-158-287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 111,194 control chromosomes in the GnomAD database, including 476 homozygotes. There are 3,348 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (476 hom., 3348 hem., cov: 22)
• Consequence: USP9X NM_001039591.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.156

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant X-41123184-G-A is Benign according to our data. Variant chrX-41123184-G-A is described in ClinVar as [Benign]. Clinvar id is 1246199.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP9X	NM_001039591.3	c.-158-287G>A		intron_variant		ENST00000378308.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9X	ENST00000378308.7	c.-158-287G>A		intron_variant		5	NM_001039591.3	P4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 11726 AN: 111138 Hom.: 476 Cov.: 22 AF XY: 0.100 AC XY: 3346 AN XY: 33390

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0659

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0882

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0899

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.105 AC: 11721 AN: 111194 Hom.: 476 Cov.: 22 AF XY: 0.100 AC XY: 3348 AN XY: 33456

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.0659

Gnomad4 EAS AF: 0.00112

Gnomad4 SAS AF: 0.0787

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0887

Alfa AF: 0.120 Hom.: 650

Bravo AF: 0.101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.37

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

Other links and lift over

dbSNP: rs1263921; hg19: chrX-40982437;