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GeneBe

19-55401601-A-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014501.3(UBE2S):c.504T>G(p.Gly168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,605,766 control chromosomes in the GnomAD database, including 261 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0093 ( 12 hom., cov: 32)
Exomes 𝑓: 0.014 ( 249 hom. )

Consequence

UBE2S
NM_014501.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.196
Variant links:
Genes affected
UBE2S (HGNC:17895): (ubiquitin conjugating enzyme E2 S) This gene encodes a member of the ubiquitin-conjugating enzyme family. The encoded protein is able to form a thiol ester linkage with ubiquitin in a ubiquitin activating enzyme-dependent manner, a characteristic property of ubiquitin carrier proteins. [provided by RefSeq, Jul 2008]
RPL28 (HGNC:10330): (ribosomal protein L28) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L28E family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 19-55401601-A-C is Benign according to our data. Variant chr19-55401601-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 781884.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.196 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00935 (1423/152204) while in subpopulation SAS AF= 0.0426 (205/4812). AF 95% confidence interval is 0.0378. There are 12 homozygotes in gnomad4. There are 732 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1423 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBE2SNM_014501.3 linkuse as main transcriptc.504T>G p.Gly168= synonymous_variant 4/4 ENST00000264552.14
RPL28NM_001363697.1 linkuse as main transcriptc.325-1342A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBE2SENST00000264552.14 linkuse as main transcriptc.504T>G p.Gly168= synonymous_variant 4/41 NM_014501.3 P1
UBE2SENST00000587845.5 linkuse as main transcriptc.591T>G p.Gly197= synonymous_variant 5/52
RPL28ENST00000560055.5 linkuse as main transcriptc.325-1342A>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00934
AC:
1421
AN:
152090
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00316
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00700
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.0160
Gnomad SAS
AF:
0.0423
Gnomad FIN
AF:
0.00857
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0115
Gnomad OTH
AF:
0.00909
GnomAD3 exomes
AF:
0.0131
AC:
3022
AN:
229992
Hom.:
50
AF XY:
0.0149
AC XY:
1900
AN XY:
127252
show subpopulations
Gnomad AFR exome
AF:
0.00237
Gnomad AMR exome
AF:
0.00689
Gnomad ASJ exome
AF:
0.00169
Gnomad EAS exome
AF:
0.0131
Gnomad SAS exome
AF:
0.0434
Gnomad FIN exome
AF:
0.00885
Gnomad NFE exome
AF:
0.00973
Gnomad OTH exome
AF:
0.00979
GnomAD4 exome
AF:
0.0142
AC:
20605
AN:
1453562
Hom.:
249
Cov.:
30
AF XY:
0.0151
AC XY:
10899
AN XY:
722932
show subpopulations
Gnomad4 AFR exome
AF:
0.00294
Gnomad4 AMR exome
AF:
0.00702
Gnomad4 ASJ exome
AF:
0.00189
Gnomad4 EAS exome
AF:
0.0242
Gnomad4 SAS exome
AF:
0.0444
Gnomad4 FIN exome
AF:
0.00898
Gnomad4 NFE exome
AF:
0.0128
Gnomad4 OTH exome
AF:
0.0123
GnomAD4 genome
AF:
0.00935
AC:
1423
AN:
152204
Hom.:
12
Cov.:
32
AF XY:
0.00984
AC XY:
732
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.00320
Gnomad4 AMR
AF:
0.00699
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.0161
Gnomad4 SAS
AF:
0.0426
Gnomad4 FIN
AF:
0.00857
Gnomad4 NFE
AF:
0.0114
Gnomad4 OTH
AF:
0.00900
Alfa
AF:
0.00668
Hom.:
3
Bravo
AF:
0.00797

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeJul 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.3
DANN
Benign
0.47

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: rs111954966; hg19: chr19-55912969; API