Variant chr1-26282328-A-AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP3

The NM_001389556.1(UBXN11):c.1533_1534insGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC(p.Gly496_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 0.0088 ( 34 hom., cov: 0)

Exomes 𝑓: 0.0061 ( 236 hom. )

Failed GnomAD Quality Control

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 Likely_benign. Variant got -1 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001389556.1

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBXN11	NM_001389556.1 linkuse as main transcript	c.1533_1534insGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC	p.Gly496_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_1534insGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC	p.Gly496_Pro511dup	inframe_insertion	15/15	5	NM_001389556.1	A2	Q5T124-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

320

AN:

36076

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0495

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0324

Gnomad SAS

AF:

0.00307

Gnomad FIN

AF:

0.00135

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00139

Gnomad OTH

AF:

0.00377

GnomAD3 exomes

AF:

0.00332

AC:

314

AN:

94654

Hom.:

AF XY:

0.00286

AC XY:

154

AN XY:

53796

show subpopulations

Gnomad AFR exome

AF:

0.000131

Gnomad AMR exome

AF:

0.0142

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0270

Gnomad SAS exome

AF:

0.000973

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000385

Gnomad OTH exome

AF:

0.00289

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00615

AC:

4561

AN:

741696

Hom.:

236

Cov.:

AF XY:

0.00643

AC XY:

2292

AN XY:

356588

show subpopulations

Gnomad4 AFR exome

AF:

0.00219

Gnomad4 AMR exome

AF:

0.0854

Gnomad4 ASJ exome

AF:

0.00194

Gnomad4 EAS exome

AF:

0.0964

Gnomad4 SAS exome

AF:

0.00318

Gnomad4 FIN exome

AF:

0.000637

Gnomad4 NFE exome

AF:

0.00105

Gnomad4 OTH exome

AF:

0.00885

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00880

AC:

318

AN:

36144

Hom.:

Cov.:

AF XY:

0.0101

AC XY:

182

AN XY:

18032

show subpopulations

Gnomad4 AFR

AF:

0.00185

Gnomad4 AMR

AF:

0.0496

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0310

Gnomad4 SAS

AF:

0.00307

Gnomad4 FIN

AF:

0.00135

Gnomad4 NFE

AF:

0.00139

Gnomad4 OTH

AF:

0.00362

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