dbSNP rs11248866: UBE2I:c.151-314G>A (chr16-1315340-G-A) – 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.151-314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 400,680 control chromosomes in the GnomAD database, including 74,023 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 0.53 ( 23681 hom., cov: 34)

Exomes 𝑓: 0.63 ( 50342 hom. )

Consequence

UBE2I
NM_003345.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

8 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:

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003345.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBE2I	NM_003345.5	MANE Select	c.151-314G>A	intron	N/A	NP_003336.1	P63279
UBE2I	NM_194259.3		c.151-314G>A	intron	N/A	NP_919235.1	P63279
UBE2I	NM_194260.3		c.151-314G>A	intron	N/A	NP_919236.1	P63279

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBE2I	ENST00000397514.8	TSL:1 MANE Select	c.151-314G>A	intron	N/A	ENSP00000380649.3	P63279
UBE2I	ENST00000567074.7	TSL:1	c.151-314G>A	intron	N/A	ENSP00000455893.2	P63279
UBE2I	ENST00000402301.6	TSL:1	n.187-314G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.531

AC:

80750

AN:

151976

Hom.:

23685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.902

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.550

GnomAD4 exome

AF:

0.625

AC:

155406

AN:

248586

Hom.:

50342

Cov.:

AF XY:

0.627

AC XY:

82332

AN XY:

131228

show subpopulations

African (AFR)

AF:

0.278

AC:

2154

AN:

7752

American (AMR)

AF:

0.556

AC:

6513

AN:

11716

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

4366

AN:

7136

East Asian (EAS)

AF:

0.897

AC:

13178

AN:

14696

South Asian (SAS)

AF:

0.644

AC:

21923

AN:

34020

European-Finnish (FIN)

AF:

0.674

AC:

8517

AN:

12644

Middle Eastern (MID)

AF:

0.563

AC:

580

AN:

1030

European-Non Finnish (NFE)

AF:

0.616

AC:

89711

AN:

145676

Other (OTH)

AF:

0.608

AC:

8464

AN:

13916

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

2614

5228

7841

10455

13069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

524

1048

1572

2096

2620

<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:

0.531

AC:

80753

AN:

152094

Hom.:

23681

Cov.:

AF XY:

0.539

AC XY:

40070

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.278

AC:

11539

AN:

41490

American (AMR)

AF:

0.555

AC:

8491

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2138

AN:

3470

East Asian (EAS)

AF:

0.902

AC:

4669

AN:

5178

South Asian (SAS)

AF:

0.667

AC:

3212

AN:

4816

European-Finnish (FIN)

AF:

0.678

AC:

7187

AN:

10602

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.613

AC:

41608

AN:

67914

Other (OTH)

AF:

0.553

AC:

1169

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1816

3632

5447

7263

9079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<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:

0.549

Hom.:

3175

Bravo

AF:

0.511

Asia WGS

AF:

0.767

AC:

2666

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.40

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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