Variant 1-26282334-TGGGGCCG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PVS1_ModerateBP6BA1

The NM_001389556.1(UBXN11):c.1521_1527delCGGCCCC(p.Gly508fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 1,163,816 control chromosomes in the GnomAD database, including 97,792 homozygotes. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.54 ( 19512 hom., cov: 0)

Exomes 𝑓: 0.47 ( 97792 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: -0.0550

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:

UBXN11 (HGNC:):

UBXN11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 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 0.0269 CDS is truncated, and there are 0 pathogenic variants in the truncated region.

BP6

Variant 1-26282334-TGGGGCCG-T is Benign according to our data. Variant chr1-26282334-TGGGGCCG-T is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBXN11	NM_001389556.1 linkuse as main transcript	c.1521_1527delCGGCCCC	p.Gly508fs	frameshift_variant	15/15	ENST00000374222.6	NP_001376485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBXN11	ENST00000374222.6 linkuse as main transcript	c.1521_1527delCGGCCCC	p.Gly508fs	frameshift_variant	15/15	5	NM_001389556.1	ENSP00000363339.1		Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

72387

AN:

133754

Hom.:

19516

Cov.:

FAILED QC

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.604

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.534

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.540

GnomAD3 exomes

AF:

0.309

AC:

32261

AN:

104566

Hom.:

3493

AF XY:

0.312

AC XY:

17914

AN XY:

57358

show subpopulations

Gnomad AFR exome

AF:

0.237

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.151

Gnomad FIN exome

AF:

0.373

Gnomad NFE exome

AF:

0.386

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.465

AC:

541475

AN:

1163816

Hom.:

97792

AF XY:

0.459

AC XY:

258019

AN XY:

561708

show subpopulations

Gnomad4 AFR exome

AF:

0.288

Gnomad4 AMR exome

AF:

0.248

Gnomad4 ASJ exome

AF:

0.419

Gnomad4 EAS exome

AF:

0.186

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.396

Gnomad4 NFE exome

AF:

0.498

Gnomad4 OTH exome

AF:

0.417

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.541

AC:

72398

AN:

133832

Hom.:

19512

Cov.:

AF XY:

0.529

AC XY:

34362

AN XY:

64936

show subpopulations

Gnomad4 AFR

AF:

0.438

Gnomad4 AMR

AF:

0.464

Gnomad4 ASJ

AF:

0.604

Gnomad4 EAS

AF:

0.290

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.635

Gnomad4 OTH

AF:

0.535

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