Variant chr6-42564319-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001363705.2(UBR2):c.-1G>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00221 in 1,609,992 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0022 ( 11 hom. )

Consequence

UBR2
NM_001363705.2 5_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.36

Variant links:

Genes affected

UBR2 (HGNC:21289): (ubiquitin protein ligase E3 component n-recognin 2) Enables leucine binding activity. Involved in cellular response to leucine and negative regulation of TOR signaling. Predicted to be located in cytosol. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. Predicted to colocalize with chromatin. [provided by Alliance of Genome Resources, Apr 2022]

UBR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 6-42564319-G-A is Benign according to our data. Variant chr6-42564319-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656552.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 302 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBR2	NM_001363705.2 linkuse as main transcript	c.-1G>A		5_prime_UTR_variant	1/47	ENST00000372901.2	NP_001350634.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
UBR2	ENST00000372901 linkuse as main transcript	c.-1G>A	5_prime_UTR_variant	1/47	5	NM_001363705.2	ENSP00000361992.1	Q8IWV8-4
UBR2	ENST00000372899 linkuse as main transcript	c.-1G>A	5_prime_UTR_variant	1/47	1		ENSP00000361990.1	Q8IWV8-1
UBR2	ENST00000372903 linkuse as main transcript	c.-1G>A	5_prime_UTR_variant	1/12	1		ENSP00000361994.2	Q8IWV8-2

Frequencies

GnomAD3 genomes

AF:

0.00198

AC:

302

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.000941

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00297

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00241

AC:

580

AN:

240882

Hom.:

AF XY:

0.00244

AC XY:

319

AN XY:

130674

show subpopulations

Gnomad AFR exome

AF:

0.000327

Gnomad AMR exome

AF:

0.00169

Gnomad ASJ exome

AF:

0.00430

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00494

Gnomad FIN exome

AF:

0.000739

Gnomad NFE exome

AF:

0.00264

Gnomad OTH exome

AF:

0.00482

GnomAD4 exome

AF:

0.00223

AC:

3255

AN:

1457628

Hom.:

Cov.:

AF XY:

0.00232

AC XY:

1685

AN XY:

724792

show subpopulations

Gnomad4 AFR exome

AF:

0.000628

Gnomad4 AMR exome

AF:

0.00157

Gnomad4 ASJ exome

AF:

0.00613

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00464

Gnomad4 FIN exome

AF:

0.000697

Gnomad4 NFE exome

AF:

0.00215

Gnomad4 OTH exome

AF:

0.00229

GnomAD4 genome

AF:

0.00198

AC:

302

AN:

152364

Hom.:

Cov.:

AF XY:

0.00197

AC XY:

147

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.000941

Gnomad4 NFE

AF:

0.00297

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00294

Hom.:

Bravo

AF:

0.00182

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

UBR2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Uncertain

0.98

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