Variant 3-23889189-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003341.5(UBE2E1):c.414T>C(p.Asn138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,613,474 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0036 ( 11 hom. )

Consequence

UBE2E1
NM_003341.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

UBE2E1 (HGNC:12477): (ubiquitin conjugating enzyme E2 E1) 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. Three alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

UBE2E1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 3-23889189-T-C is Benign according to our data. Variant chr3-23889189-T-C is described in ClinVar as [Benign]. Clinvar id is 779087.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.39 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
UBE2E1	NM_003341.5 linkuse as main transcript	c.414T>C	p.Asn138=	synonymous_variant	5/6	ENST00000306627.8
UBE2E1	NM_182666.3 linkuse as main transcript	c.363T>C	p.Asn121=	synonymous_variant	4/5
UBE2E1	NM_001202476.2 linkuse as main transcript	c.315T>C	p.Asn105=	synonymous_variant	4/5
UBE2E1	XM_005265431.6 linkuse as main transcript	c.315T>C	p.Asn105=	synonymous_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2E1	ENST00000306627.8 linkuse as main transcript	c.414T>C	p.Asn138=	synonymous_variant	5/6	1	NM_003341.5	P1	P51965-1

Frequencies

GnomAD3 genomes

AF:

0.00269

AC:

410

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00615

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00373

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00269

AC:

676

AN:

251144

Hom.:

AF XY:

0.00277

AC XY:

376

AN XY:

135776

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.000198

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00111

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.00424

Gnomad OTH exome

AF:

0.00425

GnomAD4 exome

AF:

0.00360

AC:

5261

AN:

1461108

Hom.:

Cov.:

AF XY:

0.00354

AC XY:

2571

AN XY:

726894

show subpopulations

Gnomad4 AFR exome

AF:

0.000837

Gnomad4 AMR exome

AF:

0.00329

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00117

Gnomad4 FIN exome

AF:

0.000244

Gnomad4 NFE exome

AF:

0.00421

Gnomad4 OTH exome

AF:

0.00373

GnomAD4 genome

AF:

0.00268

AC:

409

AN:

152366

Hom.:

Cov.:

AF XY:

0.00243

AC XY:

181

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.00103

Gnomad4 AMR

AF:

0.00614

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00373

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00320

Hom.:

Bravo

AF:

0.00342

Asia WGS

AF:

0.000578

AC:

AN:

3476

EpiCase

AF:

0.00360

EpiControl

AF:

0.00504

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

Invitae

May 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

5.0

DANN

Benign

0.76

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