dbSNP rs7187167: UBE2I:c.-259-2719T>C (chr16-1299208-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000852849.1(UBE2I):c.-259-2719T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,016 control chromosomes in the GnomAD database, including 36,730 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 0.69 ( 36709 hom., cov: 32)

Exomes 𝑓: 0.76 ( 21 hom. )

Consequence

UBE2I
ENST00000852849.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.770

Publications

26 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:

UBE2I-AS1 (HGNC:58131):

UBE2I-AS1 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000852849.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
UBE2I-AS1	NR_198995.1	n.398A>G	non_coding_transcript_exon	Exon 1 of 3
UBE2I-AS1	NR_198996.1	n.398A>G	non_coding_transcript_exon	Exon 1 of 2
UBE2I-AS1	NR_198997.1	n.398A>G	non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UBE2I	ENST00000852849.1		c.-259-2719T>C	intron	N/A	ENSP00000522908.1
UBE2I-AS1	ENST00000561649.4	TSL:3	n.428A>G	non_coding_transcript_exon	Exon 1 of 3
UBE2I-AS1	ENST00000686290.3		n.362A>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.691

AC:

104917

AN:

151826

Hom.:

36697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.750

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.776

Gnomad FIN

AF:

0.769

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.720

Gnomad OTH

AF:

0.672

GnomAD4 exome

AF:

0.764

AC:

AN:

Hom.:

Cov.:

AF XY:

0.725

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.696

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.691

AC:

104976

AN:

151944

Hom.:

36709

Cov.:

AF XY:

0.695

AC XY:

51634

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.599

AC:

24776

AN:

41374

American (AMR)

AF:

0.647

AC:

9871

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2505

AN:

3470

East Asian (EAS)

AF:

0.911

AC:

4712

AN:

5172

South Asian (SAS)

AF:

0.776

AC:

3738

AN:

4820

European-Finnish (FIN)

AF:

0.769

AC:

8128

AN:

10564

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.720

AC:

48950

AN:

67976

Other (OTH)

AF:

0.674

AC:

1419

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1620

3240

4861

6481

8101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.711

Hom.:

106691

Bravo

AF:

0.675

Asia WGS

AF:

0.833

AC:

2898

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.5

(source)

DANN

Benign

0.35

PhyloP100

-0.77

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over