Variant chr20-3110238-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000217173.7(UBOX5):c.1494G>T(p.Pro498Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 1,614,068 control chromosomes in the GnomAD database, including 164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.012 ( 17 hom., cov: 33)

Exomes 𝑓: 0.014 ( 147 hom. )

Consequence

UBOX5
ENST00000217173.7 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.36

Variant links:

Genes affected

UBOX5 (HGNC:17777): (U-box domain containing 5) This gene encodes a U-box domain containing protein. The encoded protein interacts with E2 enzymes and may play a role in the ubiquitination pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

UBOX5 links:

UBOX5-AS1 (HGNC:):

UBOX5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 20-3110238-C-A is Benign according to our data. Variant chr20-3110238-C-A is described in ClinVar as [Benign]. Clinvar id is 3024835.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.36 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBOX5	NM_014948.4 linkuse as main transcript	c.1494G>T	p.Pro498Pro	synonymous_variant	5/5	ENST00000217173.7	NP_055763.1	O94941-1
UBOX5	NM_001267584.2 linkuse as main transcript	c.1489G>T	p.Gly497Cys	missense_variant	5/5		NP_001254513.1
UBOX5	NM_199415.3 linkuse as main transcript	c.1332G>T	p.Pro444Pro	synonymous_variant	4/4		NP_955447.1	O94941-2
UBOX5-AS1	NR_038395.1 linkuse as main transcript	n.938-40C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
UBOX5	ENST00000217173.7 linkuse as main transcript	c.1494G>T	p.Pro498Pro	synonymous_variant	5/5	1	NM_014948.4	ENSP00000217173.2	O94941-1
UBOX5	ENST00000348031.6 linkuse as main transcript	c.1332G>T	p.Pro444Pro	synonymous_variant	4/4	1		ENSP00000311726.3	O94941-2
UBOX5-AS1	ENST00000446537.5 linkuse as main transcript	n.936-40C>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0120

AC:

1823

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00299

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0114

Gnomad ASJ

AF:

0.0147

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.0330

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0151

Gnomad OTH

AF:

0.00765

GnomAD3 exomes

AF:

0.0124

AC:

3114

AN:

251458

Hom.:

AF XY:

0.0125

AC XY:

1693

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00457

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.00190

Gnomad SAS exome

AF:

0.0120

Gnomad FIN exome

AF:

0.0287

Gnomad NFE exome

AF:

0.0148

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.0136

AC:

19863

AN:

1461774

Hom.:

147

Cov.:

AF XY:

0.0136

AC XY:

9867

AN XY:

727174

show subpopulations

Gnomad4 AFR exome

AF:

0.00200

Gnomad4 AMR exome

AF:

0.00458

Gnomad4 ASJ exome

AF:

0.0142

Gnomad4 EAS exome

AF:

0.00214

Gnomad4 SAS exome

AF:

0.0127

Gnomad4 FIN exome

AF:

0.0266

Gnomad4 NFE exome

AF:

0.0143

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.0120

AC:

1824

AN:

152294

Hom.:

Cov.:

AF XY:

0.0129

AC XY:

964

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00298

Gnomad4 AMR

AF:

0.0114

Gnomad4 ASJ

AF:

0.0147

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.0122

Gnomad4 FIN

AF:

0.0330

Gnomad4 NFE

AF:

0.0151

Gnomad4 OTH

AF:

0.00757

Alfa

AF:

0.0109

Hom.:

Bravo

AF:

0.00976

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0116

EpiControl

AF:

0.0133

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2024

UBOX5: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.094

DANN

Benign

0.85

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