rs34606078

Variant names:

• chr20-3110238-C-A
• rs34606078
• NM_014948.4:c.1494G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-3110238-C-A
• chr20-3110238-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001267584.2(UBOX5):​c.1489G>T​(p.Gly497Cys) variant causes a missense 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. 5/6 in silico tools predict 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 NM_001267584.2 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.36

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-AS1 (HGNC:44111): (UBOX5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 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.
• BS2: High Homozygotes in GnomAd4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBOX5	NM_014948.4	c.1494G>T	p.Pro498Pro	synonymous_variant	Exon 5 of 5	ENST00000217173.7	NP_055763.1
UBOX5	NM_001267584.2	c.1489G>T	p.Gly497Cys	missense_variant	Exon 5 of 5		NP_001254513.1
UBOX5	NM_199415.3	c.1332G>T	p.Pro444Pro	synonymous_variant	Exon 4 of 4		NP_955447.1
UBOX5-AS1	NR_038395.1	n.938-40C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBOX5	ENST00000217173.7	c.1494G>T	p.Pro498Pro	synonymous_variant	Exon 5 of 5	1	NM_014948.4	ENSP00000217173.2
UBOX5	ENST00000348031.6	c.1332G>T	p.Pro444Pro	synonymous_variant	Exon 4 of 4	1		ENSP00000311726.3
UBOX5-AS1	ENST00000446537.5	n.936-40C>A		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.0120 AC: 1823 AN: 152176 Hom.: 17 Cov.: 33

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.: 22 AF XY: 0.0125 AC XY: 1693 AN XY: 135918

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.: 33 AF XY: 0.0136 AC XY: 9867 AN XY: 727174

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.: 17 Cov.: 33 AF XY: 0.0129 AC XY: 964 AN XY: 74468

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.: 3

Bravo AF: 0.00976

Asia WGS AF: 0.00375 AC: 13 AN: 3478

EpiCase AF: 0.0116

EpiControl AF: 0.0133

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Other links and lift over

dbSNP: rs34606078; hg19: chr20-3090884;