Variant 16-1314364-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_003345.5(UBE2I):c.138A>G(p.Pro46=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,613,488 control chromosomes in the GnomAD database, including 19,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1895 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17613 hom. )

Consequence

UBE2I
NM_003345.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.253

Variant links:

Genes affected

UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

UBE2I links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 16-1314364-A-G is Benign according to our data. Variant chr16-1314364-A-G is described in ClinVar as [Benign]. Clinvar id is 1249830.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.253 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2I	NM_003345.5 linkuse as main transcript	c.138A>G	p.Pro46=	synonymous_variant	3/7	ENST00000397514.8	NP_003336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2I	ENST00000397514.8 linkuse as main transcript	c.138A>G	p.Pro46=	synonymous_variant	3/7	1	NM_003345.5	ENSP00000380649	P1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22884

AN:

152008

Hom.:

1892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.0397

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.155

AC:

38967

AN:

250794

Hom.:

3730

AF XY:

0.150

AC XY:

20383

AN XY:

135770

show subpopulations

Gnomad AFR exome

AF:

0.164

Gnomad AMR exome

AF:

0.303

Gnomad ASJ exome

AF:

0.0696

Gnomad EAS exome

AF:

0.0495

Gnomad SAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.143

Gnomad OTH exome

AF:

0.145

GnomAD4 exome

AF:

0.150

AC:

218812

AN:

1461362

Hom.:

17613

Cov.:

AF XY:

0.148

AC XY:

107670

AN XY:

727006

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.291

Gnomad4 ASJ exome

AF:

0.0689

Gnomad4 EAS exome

AF:

0.0406

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.151

AC:

22908

AN:

152126

Hom.:

1895

Cov.:

AF XY:

0.151

AC XY:

11196

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.0396

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.150

Hom.:

1508

Bravo

AF:

0.159

Asia WGS

AF:

0.0770

AC:

267

AN:

3478

EpiCase

AF:

0.141

EpiControl

AF:

0.137

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 06, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.1

DANN

Benign

0.59

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