Variant 1-26282328-AGGGACTGGGGCCGGGACCGGGACC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3BA1

The NM_001389556.1(UBXN11):c.1510_1533del(p.Gly504_Pro511del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 764,054 control chromosomes in the GnomAD database, including 715 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.061 ( 41 hom., cov: 0)

Exomes 𝑓: 0.020 ( 674 hom. )

Consequence

UBXN11
NM_001389556.1 inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:2

Conservation

PhyloP100: 0.00600

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 Benign. Variant got -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001389556.1

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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.1510_1533del	p.Gly504_Pro511del	inframe_deletion	15/15	ENST00000374222.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN11	ENST00000374222.6 linkuse as main transcript	c.1510_1533del	p.Gly504_Pro511del	inframe_deletion	15/15	5	NM_001389556.1	A2	Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

2201

AN:

36020

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0241

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0423

Gnomad ASJ

AF:

0.0295

Gnomad EAS

AF:

0.0825

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0642

Gnomad MID

AF:

0.0500

Gnomad NFE

AF:

0.0841

Gnomad OTH

AF:

0.0526

GnomAD3 exomes

AF:

0.0281

AC:

2658

AN:

94654

Hom.:

438

AF XY:

0.0287

AC XY:

1544

AN XY:

53796

show subpopulations

Gnomad AFR exome

AF:

0.00850

Gnomad AMR exome

AF:

0.0197

Gnomad ASJ exome

AF:

0.00555

Gnomad EAS exome

AF:

0.0958

Gnomad SAS exome

AF:

0.0756

Gnomad FIN exome

AF:

0.0182

Gnomad NFE exome

AF:

0.0184

Gnomad OTH exome

AF:

0.0231

GnomAD4 exome

AF:

0.0202

AC:

14725

AN:

727972

Hom.:

674

AF XY:

0.0231

AC XY:

8071

AN XY:

350126

show subpopulations

Gnomad4 AFR exome

AF:

0.00585

Gnomad4 AMR exome

AF:

0.0208

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.0616

Gnomad4 SAS exome

AF:

0.0806

Gnomad4 FIN exome

AF:

0.0413

Gnomad4 NFE exome

AF:

0.0139

Gnomad4 OTH exome

AF:

0.0215

GnomAD4 genome

AF:

0.0610

AC:

2201

AN:

36082

Hom.:

Cov.:

AF XY:

0.0630

AC XY:

1135

AN XY:

18006

show subpopulations

Gnomad4 AFR

AF:

0.0240

Gnomad4 AMR

AF:

0.0422

Gnomad4 ASJ

AF:

0.0295

Gnomad4 EAS

AF:

0.0828

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.0642

Gnomad4 NFE

AF:

0.0841

Gnomad4 OTH

AF:

0.0542

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