Variant 1-26282374-ACC-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.1486_1487del(p.Gly496SerfsTer?) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 601,844 control chromosomes in the GnomAD database, including 13,135 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 2261 hom., cov: 0)

Exomes 𝑓: 0.26 ( 10874 hom. )

Consequence

UBXN11
NM_001389556.1 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:3

Conservation

PhyloP100: -0.135

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:

Genome browser will be placed here

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 0.0493 CDS is truncated, and there are 0 pathogenic variants in the truncated region.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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.1486_1487del	p.Gly496SerfsTer?	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.1486_1487del	p.Gly496SerfsTer?	frameshift_variant	15/15	5	NM_001389556.1	A2	Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

22046

AN:

76750

Hom.:

2255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.295

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.299

GnomAD3 exomes

AF:

0.0435

AC:

4550

AN:

104586

Hom.:

618

AF XY:

0.0445

AC XY:

2552

AN XY:

57410

show subpopulations

Gnomad AFR exome

AF:

0.0708

Gnomad AMR exome

AF:

0.0352

Gnomad ASJ exome

AF:

0.0432

Gnomad EAS exome

AF:

0.0231

Gnomad SAS exome

AF:

0.0475

Gnomad FIN exome

AF:

0.0528

Gnomad NFE exome

AF:

0.0428

Gnomad OTH exome

AF:

0.0461

GnomAD4 exome

AF:

0.265

AC:

139082

AN:

525038

Hom.:

10874

AF XY:

0.268

AC XY:

69735

AN XY:

260558

show subpopulations

Gnomad4 AFR exome

AF:

0.351

Gnomad4 AMR exome

AF:

0.196

Gnomad4 ASJ exome

AF:

0.352

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.296

Gnomad4 FIN exome

AF:

0.358

Gnomad4 NFE exome

AF:

0.258

Gnomad4 OTH exome

AF:

0.283

GnomAD4 genome

AF:

0.287

AC:

22060

AN:

76806

Hom.:

2261

Cov.:

AF XY:

0.294

AC XY:

11035

AN XY:

37484

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.305

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.292

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Small cell lung carcinoma

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

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

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.

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