dbSNP rs10497353: UBR3:c.5200-2549G>T (chr2-170077265-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_172070.4(UBR3):c.5200-2549G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 740,068 control chromosomes in the GnomAD database, including 684 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.051 ( 381 hom., cov: 32)

Exomes 𝑓: 0.022 ( 303 hom. )

Consequence

UBR3
NM_172070.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.460

Publications

1 publications found

Variant links:

Genes affected

UBR3 (HGNC:30467): (ubiquitin protein ligase E3 component n-recognin 3) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including cellular protein metabolic process; sensory perception of smell; and suckling behavior. Predicted to act upstream of or within in utero embryonic development and olfactory behavior. Predicted to be integral component of membrane. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

UBR3 links:

NSA2P5 (HGNC:54584): (NSA2 pseudogene 5)

NSA2P5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172070.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBR3	NM_172070.4	MANE Select	c.5200-2549G>T		intron	N/A	NP_742067.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBR3	ENST00000272793.11	TSL:5 MANE Select	c.5200-2549G>T	intron	N/A	ENSP00000272793.5	Q6ZT12-1
UBR3	ENST00000474426.1	TSL:1	n.1311-2549G>T	intron	N/A
UBR3	ENST00000949146.1		c.5233-2627G>T	intron	N/A	ENSP00000619205.1

Frequencies

GnomAD3 genomes

AF:

0.0508

AC:

7728

AN:

152094

Hom.:

380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0358

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.0116

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0200

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.0397

GnomAD4 exome

AF:

0.0216

AC:

12708

AN:

587856

Hom.:

303

Cov.:

AF XY:

0.0201

AC XY:

6468

AN XY:

322230

show subpopulations

African (AFR)

AF:

0.123

AC:

2017

AN:

16378

American (AMR)

AF:

0.0488

AC:

2056

AN:

42096

Ashkenazi Jewish (ASJ)

AF:

0.00542

AC:

106

AN:

19572

East Asian (EAS)

AF:

0.0182

AC:

599

AN:

32976

South Asian (SAS)

AF:

0.0161

AC:

1115

AN:

69174

European-Finnish (FIN)

AF:

0.0183

AC:

900

AN:

49172

Middle Eastern (MID)

AF:

0.0154

AC:

AN:

3120

European-Non Finnish (NFE)

AF:

0.0157

AC:

5115

AN:

325216

Other (OTH)

AF:

0.0249

AC:

752

AN:

30152

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.411

Heterozygous variant carriers

415

830

1244

1659

2074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0508

AC:

7734

AN:

152212

Hom.:

381

Cov.:

AF XY:

0.0492

AC XY:

3658

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.132

AC:

5466

AN:

41524

American (AMR)

AF:

0.0356

AC:

545

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00461

AC:

AN:

3470

East Asian (EAS)

AF:

0.0116

AC:

AN:

5176

South Asian (SAS)

AF:

0.0195

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0200

AC:

212

AN:

10612

Middle Eastern (MID)

AF:

0.0171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0184

AC:

1252

AN:

68002

Other (OTH)

AF:

0.0397

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

348

696

1045

1393

1741

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0408

Hom.:

Bravo

AF:

0.0571

Asia WGS

AF:

0.0310

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

4.2

(source)

DANN

Benign

0.65

PhyloP100

0.46

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over