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16-1314364-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_003345.5(UBE2I):c.138A>G(p.Pro46=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,613,488 control chromosomes in the GnomAD database, including 19,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 1895 hom., cov: 33)
Exomes 𝑓: 0.15 ( 17613 hom. )

Consequence

UBE2I
NM_003345.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.253
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-1314364-A-G is Benign according to our data. Variant chr16-1314364-A-G is described in ClinVar as [Benign]. Clinvar id is 1249830.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.253 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBE2INM_003345.5 linkuse as main transcriptc.138A>G p.Pro46= synonymous_variant 3/7 ENST00000397514.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBE2IENST00000397514.8 linkuse as main transcriptc.138A>G p.Pro46= synonymous_variant 3/71 NM_003345.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.151
AC:
22884
AN:
152008
Hom.:
1892
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.158
Gnomad AMI
AF:
0.0560
Gnomad AMR
AF:
0.226
Gnomad ASJ
AF:
0.0706
Gnomad EAS
AF:
0.0397
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.133
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.148
GnomAD3 exomes
AF:
0.155
AC:
38967
AN:
250794
Hom.:
3730
AF XY:
0.150
AC XY:
20383
AN XY:
135770
show subpopulations
Gnomad AFR exome
AF:
0.164
Gnomad AMR exome
AF:
0.303
Gnomad ASJ exome
AF:
0.0696
Gnomad EAS exome
AF:
0.0495
Gnomad SAS exome
AF:
0.140
Gnomad FIN exome
AF:
0.130
Gnomad NFE exome
AF:
0.143
Gnomad OTH exome
AF:
0.145
GnomAD4 exome
AF:
0.150
AC:
218812
AN:
1461362
Hom.:
17613
Cov.:
36
AF XY:
0.148
AC XY:
107670
AN XY:
727006
show subpopulations
Gnomad4 AFR exome
AF:
0.158
Gnomad4 AMR exome
AF:
0.291
Gnomad4 ASJ exome
AF:
0.0689
Gnomad4 EAS exome
AF:
0.0406
Gnomad4 SAS exome
AF:
0.146
Gnomad4 FIN exome
AF:
0.131
Gnomad4 NFE exome
AF:
0.152
Gnomad4 OTH exome
AF:
0.136
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.151
AC:
22908
AN:
152126
Hom.:
1895
Cov.:
33
AF XY:
0.151
AC XY:
11196
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.157
Gnomad4 AMR
AF:
0.226
Gnomad4 ASJ
AF:
0.0706
Gnomad4 EAS
AF:
0.0396
Gnomad4 SAS
AF:
0.139
Gnomad4 FIN
AF:
0.133
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.149
Alfa
AF:
0.150
Hom.:
1508
Bravo
AF:
0.159
Asia WGS
AF:
0.0770
AC:
267
AN:
3478
EpiCase
AF:
0.141
EpiControl
AF:
0.137

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 submitterclinical testingGeneDxMay 06, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
3.1
Dann
Benign
0.59

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.

Other links and lift over

dbSNP: rs4610; hg19: chr16-1364365; COSMIC: COSV57647027; COSMIC: COSV57647027; API