chr16-1320302-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003345.5(UBE2I):c.333+19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 1,612,110 control chromosomes in the GnomAD database, including 643,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.92 ( 64097 hom., cov: 31)
Exomes 𝑓: 0.89 ( 579067 hom. )
Consequence
UBE2I
NM_003345.5 intron
NM_003345.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.556
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 16-1320302-T-C is Benign according to our data. Variant chr16-1320302-T-C is described in ClinVar as [Benign]. Clinvar id is 1260109.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBE2I | NM_003345.5 | c.333+19T>C | intron_variant | ENST00000397514.8 | NP_003336.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBE2I | ENST00000397514.8 | c.333+19T>C | intron_variant | 1 | NM_003345.5 | ENSP00000380649 | P1 | |||
ENST00000567829.1 | n.515A>G | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.918 AC: 139308AN: 151806Hom.: 64033 Cov.: 31
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GnomAD3 exomes AF: 0.918 AC: 229492AN: 249876Hom.: 105615 AF XY: 0.916 AC XY: 123823AN XY: 135206
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GnomAD4 exome AF: 0.890 AC: 1299452AN: 1460186Hom.: 579067 Cov.: 38 AF XY: 0.891 AC XY: 646937AN XY: 726360
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GnomAD4 genome AF: 0.918 AC: 139431AN: 151924Hom.: 64097 Cov.: 31 AF XY: 0.921 AC XY: 68322AN XY: 74220
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at