Variant 3-23887582-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_003341.5(UBE2E1):c.219C>T(p.Gly73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00926 in 1,611,076 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0056 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0096 ( 78 hom. )

Consequence

UBE2E1
NM_003341.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.17

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 3-23887582-C-T is Benign according to our data. Variant chr3-23887582-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 781706.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.17 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
UBE2E1	NM_003341.5 linkuse as main transcript	c.219C>T	p.Gly73=	synonymous_variant	4/6	ENST00000306627.8
UBE2E1	NM_182666.3 linkuse as main transcript	c.168C>T	p.Gly56=	synonymous_variant	3/5
UBE2E1	NM_001202476.2 linkuse as main transcript	c.120C>T	p.Gly40=	synonymous_variant	3/5
UBE2E1	XM_005265431.6 linkuse as main transcript	c.120C>T	p.Gly40=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2E1	ENST00000306627.8 linkuse as main transcript	c.219C>T	p.Gly73=	synonymous_variant	4/6	1	NM_003341.5	P1	P51965-1

Frequencies

GnomAD3 genomes

AF:

0.00565

AC:

860

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00445

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00340

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00955

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00556

AC:

1380

AN:

247992

Hom.:

AF XY:

0.00566

AC XY:

759

AN XY:

134040

show subpopulations

Gnomad AFR exome

AF:

0.00179

Gnomad AMR exome

AF:

0.00626

Gnomad ASJ exome

AF:

0.00302

Gnomad EAS exome

AF:

0.0000549

Gnomad SAS exome

AF:

0.000202

Gnomad FIN exome

AF:

0.00195

Gnomad NFE exome

AF:

0.00902

Gnomad OTH exome

AF:

0.00742

GnomAD4 exome

AF:

0.00964

AC:

14064

AN:

1458828

Hom.:

Cov.:

AF XY:

0.00935

AC XY:

6782

AN XY:

725672

show subpopulations

Gnomad4 AFR exome

AF:

0.00150

Gnomad4 AMR exome

AF:

0.00581

Gnomad4 ASJ exome

AF:

0.00238

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000187

Gnomad4 FIN exome

AF:

0.00197

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.00936

GnomAD4 genome

AF:

0.00564

AC:

859

AN:

152248

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

385

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00212

Gnomad4 AMR

AF:

0.00438

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00340

Gnomad4 NFE

AF:

0.00955

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00740

Hom.:

Bravo

AF:

0.00611

EpiCase

AF:

0.00987

EpiControl

AF:

0.0105

ClinVar

Significance: Benign/Likely 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	clinical testing	Invitae	May 04, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2022	UBE2E1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

8.4

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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