Variant 1-26282344-ACCGGGACCGGGACTGGG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1

The NM_001389556.1(UBXN11):c.1501_1517del(p.Pro501SerfsTer?) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 1,147,394 control chromosomes in the GnomAD database, including 98,365 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.64 ( 19461 hom., cov: 0)

Exomes 𝑓: 0.47 ( 98365 hom. )

Failed GnomAD Quality Control

Consequence

UBXN11
NM_001389556.1 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:2

Conservation

PhyloP100: 0.642

Variant links:

Genes affected

UBXN11 (HGNC:30600): (UBX domain protein 11) This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

UBXN11 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0397 CDS is truncated, and there are 0 pathogenic variants in the truncated region.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBXN11	NM_001389556.1 linkuse as main transcript	c.1501_1517del	p.Pro501SerfsTer?	frameshift_variant	15/15	ENST00000374222.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN11	ENST00000374222.6 linkuse as main transcript	c.1501_1517del	p.Pro501SerfsTer?	frameshift_variant	15/15	5	NM_001389556.1	A2	Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

72150

AN:

112334

Hom.:

19465

Cov.:

FAILED QC

Gnomad AFR

AF:

0.577

Gnomad AMI

AF:

0.706

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.615

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.640

GnomAD3 exomes

AF:

0.334

AC:

32135

AN:

96310

Hom.:

3558

AF XY:

0.338

AC XY:

17815

AN XY:

52742

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.363

Gnomad EAS exome

AF:

0.142

Gnomad SAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.419

Gnomad NFE exome

AF:

0.424

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.471

AC:

540475

AN:

1147394

Hom.:

98365

AF XY:

0.465

AC XY:

257455

AN XY:

553368

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.426

Gnomad4 EAS exome

AF:

0.182

Gnomad4 SAS exome

AF:

0.246

Gnomad4 FIN exome

AF:

0.404

Gnomad4 NFE exome

AF:

0.503

Gnomad4 OTH exome

AF:

0.424

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.642

AC:

72160

AN:

112380

Hom.:

19461

Cov.:

AF XY:

0.633

AC XY:

34226

AN XY:

54030

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.690

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.659

Gnomad4 NFE

AF:

0.713

Gnomad4 OTH

AF:

0.634

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Lung cancer

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Hepatocellular carcinoma

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

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