1-10103090-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001105562.3(UBE4B):c.578A>G(p.Glu193Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00101 in 1,602,338 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00080 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0010 ( 2 hom. )
Consequence
UBE4B
NM_001105562.3 missense, splice_region
NM_001105562.3 missense, splice_region
Scores
1
4
13
Splicing: ADA: 0.005145
2
Clinical Significance
Conservation
PhyloP100: 7.05
Genes affected
UBE4B (HGNC:12500): (ubiquitination factor E4B) 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 an additional conjugation factor, E4, which is involved in multiubiquitin chain assembly. This gene is also the strongest candidate in the neuroblastoma tumor suppressor genes. Alternatively spliced transcript variants encoding distinct isoforms 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 -7 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, UBE4B
BP4
?
Computational evidence support a benign effect (MetaRNN=0.03860143).
BS2
?
High AC in GnomAd at 121 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE4B | NM_001105562.3 | c.578A>G | p.Glu193Gly | missense_variant, splice_region_variant | 5/28 | ENST00000343090.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE4B | ENST00000343090.11 | c.578A>G | p.Glu193Gly | missense_variant, splice_region_variant | 5/28 | 1 | NM_001105562.3 | ||
UBE4B | ENST00000253251.12 | c.578A>G | p.Glu193Gly | missense_variant, splice_region_variant | 5/27 | 1 | P1 | ||
UBE4B | ENST00000672724.1 | c.578A>G | p.Glu193Gly | missense_variant, splice_region_variant | 5/29 | ||||
UBE4B | ENST00000462658.1 | n.478A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000795 AC: 121AN: 152120Hom.: 0 Cov.: 30
GnomAD3 genomes
?
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152120
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GnomAD3 exomes AF: 0.000757 AC: 188AN: 248322Hom.: 1 AF XY: 0.000781 AC XY: 105AN XY: 134412
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GnomAD4 exome AF: 0.00104 AC: 1504AN: 1450218Hom.: 2 Cov.: 30 AF XY: 0.00104 AC XY: 747AN XY: 720530
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GnomAD4 genome ? AF: 0.000795 AC: 121AN: 152120Hom.: 0 Cov.: 30 AF XY: 0.000713 AC XY: 53AN XY: 74304
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ExAC
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100
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.578A>G (p.E193G) alteration is located in exon 5 (coding exon 5) of the UBE4B gene. This alteration results from a A to G substitution at nucleotide position 578, causing the glutamic acid (E) at amino acid position 193 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
0.35
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at