Variant chr1-26282328-A-AGGGACTGGGGCCGGGACCGGGACC 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.1533_1534insGGTCCCGGTCCCGGCCCCAGTCCC(p.Gly504_Pro511dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.084 ( 183 hom., cov: 0)

Exomes 𝑓: 0.026 ( 1982 hom. )

Consequence

UBXN11
NM_001389556.1 inframe_insertion

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:

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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 (EAS) allele frequency at 95% confidence interval = 0.29 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.1533_1534insGGTCCCGGTCCCGGCCCCAGTCCC	p.Gly504_Pro511dup	inframe_insertion	15/15	ENST00000374222.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN11	ENST00000374222.6 linkuse as main transcript	c.1533_1534insGGTCCCGGTCCCGGCCCCAGTCCC	p.Gly504_Pro511dup	inframe_insertion	15/15	5	NM_001389556.1	A2	Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.0833

AC:

2865

AN:

34400

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0883

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0833

Gnomad NFE

AF:

0.0255

Gnomad OTH

AF:

0.102

GnomAD3 exomes

AF:

0.0232

AC:

2192

AN:

94654

Hom.:

258

AF XY:

0.0221

AC XY:

1190

AN XY:

53796

show subpopulations

Gnomad AFR exome

AF:

0.0215

Gnomad AMR exome

AF:

0.0379

Gnomad ASJ exome

AF:

0.00198

Gnomad EAS exome

AF:

0.204

Gnomad SAS exome

AF:

0.0378

Gnomad FIN exome

AF:

0.00442

Gnomad NFE exome

AF:

0.00209

Gnomad OTH exome

AF:

0.0188

GnomAD4 exome

AF:

0.0259

AC:

19141

AN:

738720

Hom.:

1982

Cov.:

AF XY:

0.0298

AC XY:

10575

AN XY:

354678

show subpopulations

Gnomad4 AFR exome

AF:

0.0384

Gnomad4 AMR exome

AF:

0.0963

Gnomad4 ASJ exome

AF:

0.0203

Gnomad4 EAS exome

AF:

0.326

Gnomad4 SAS exome

AF:

0.0927

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.00421

Gnomad4 OTH exome

AF:

0.0403

GnomAD4 genome

AF:

0.0835

AC:

2878

AN:

34454

Hom.:

183

Cov.:

AF XY:

0.0854

AC XY:

1465

AN XY:

17160

show subpopulations

Gnomad4 AFR

AF:

0.0888

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0409

Gnomad4 EAS

AF:

0.311

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.0255

Gnomad4 OTH

AF:

0.118

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