X-41123957-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001039591.3(USP9X):c.96+233T>C variant causes a intron 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 Benign (★).

• Frequency:
  • Genomes: 𝑓 0.67 (17577 hom., 20578 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: USP9X NM_001039591.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.85

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant X-41123957-T-C is Benign according to our data. Variant chrX-41123957-T-C is described in ClinVar as [Benign]. Clinvar id is 1273629.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 17571 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP9X	NM_001039591.3	c.96+233T>C		intron_variant		ENST00000378308.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP9X	ENST00000378308.7	c.96+233T>C		intron_variant		5	NM_001039591.3	P4

Frequencies

GnomAD3 genomes AF: 0.668 AC: 72638 AN: 108697 Hom.: 17571 Cov.: 21 AF XY: 0.661 AC XY: 20528 AN XY: 31033

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.692

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.668 AC: 72694 AN: 108753 Hom.: 17577 Cov.: 21 AF XY: 0.662 AC XY: 20578 AN XY: 31099

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.694

Alfa AF: 0.633 Hom.: 4656

Bravo AF: 0.677

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 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.096
Dann	Benign	0.47

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: rs5917408; hg19: chrX-40983210;