Genetic Variant UBE2I:c.*24A>G (chr16-1324817-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003345.5(UBE2I):c.*24A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 1,612,504 control chromosomes in the GnomAD database, including 400,842 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 0.64 ( 32324 hom., cov: 31)

Exomes 𝑓: 0.71 ( 368518 hom. )

Consequence

UBE2I
NM_003345.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.663

Publications

41 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2I	NM_003345.5 link	c.*24A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000397514.8	NP_003336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2I	ENST00000397514.8 link	c.*24A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_003345.5	ENSP00000380649.3

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

96576

AN:

151842

Hom.:

32320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.417

Gnomad AMI

AF:

0.836

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.807

Gnomad EAS

AF:

0.956

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.697

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.678

GnomAD2 exomes

AF:

0.708

AC:

177362

AN:

250376

AF XY:

0.716

show subpopulations

Gnomad AFR exome

AF:

0.415

Gnomad AMR exome

AF:

0.632

Gnomad ASJ exome

AF:

0.805

Gnomad EAS exome

AF:

0.947

Gnomad FIN exome

AF:

0.703

Gnomad NFE exome

AF:

0.719

Gnomad OTH exome

AF:

0.725

GnomAD4 exome

AF:

0.707

AC:

1032257

AN:

1460544

Hom.:

368518

Cov.:

AF XY:

0.709

AC XY:

515274

AN XY:

726570

show subpopulations

African (AFR)

AF:

0.413

AC:

13825

AN:

33450

American (AMR)

AF:

0.634

AC:

28257

AN:

44580

Ashkenazi Jewish (ASJ)

AF:

0.806

AC:

21063

AN:

26122

East Asian (EAS)

AF:

0.957

AC:

37966

AN:

39678

South Asian (SAS)

AF:

0.727

AC:

62687

AN:

86188

European-Finnish (FIN)

AF:

0.705

AC:

37551

AN:

53230

Middle Eastern (MID)

AF:

0.750

AC:

4322

AN:

5762

European-Non Finnish (NFE)

AF:

0.705

AC:

783703

AN:

1111196

Other (OTH)

AF:

0.711

AC:

42883

AN:

60338

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

14784

29568

44352

59136

73920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19668

39336

59004

78672

98340

<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:

0.636

AC:

96605

AN:

151960

Hom.:

32324

Cov.:

AF XY:

0.640

AC XY:

47535

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.417

AC:

17284

AN:

41418

American (AMR)

AF:

0.651

AC:

9928

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.807

AC:

2797

AN:

3466

East Asian (EAS)

AF:

0.956

AC:

4939

AN:

5166

South Asian (SAS)

AF:

0.738

AC:

3555

AN:

4816

European-Finnish (FIN)

AF:

0.697

AC:

7362

AN:

10570

Middle Eastern (MID)

AF:

0.796

AC:

234

AN:

294

European-Non Finnish (NFE)

AF:

0.711

AC:

48312

AN:

67960

Other (OTH)

AF:

0.681

AC:

1432

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1665

3330

4996

6661

8326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<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:

0.692

Hom.:

67542

Bravo

AF:

0.623

Asia WGS

AF:

0.846

AC:

2938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.8

(source)

DANN

Benign

0.56

PhyloP100

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over