chr3-23887582-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003341.5(UBE2E1):c.219C>T(p.Gly73=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00926 in 1,611,076 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0056 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0096 ( 78 hom. )
Consequence
UBE2E1
NM_003341.5 synonymous
NM_003341.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.17
Genes affected
UBE2E1 (HGNC:12477): (ubiquitin conjugating enzyme E2 E1) 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. Three alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 3-23887582-C-T is Benign according to our data. Variant chr3-23887582-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 781706.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.17 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE2E1 | NM_003341.5 | c.219C>T | p.Gly73= | synonymous_variant | 4/6 | ENST00000306627.8 | |
UBE2E1 | NM_182666.3 | c.168C>T | p.Gly56= | synonymous_variant | 3/5 | ||
UBE2E1 | NM_001202476.2 | c.120C>T | p.Gly40= | synonymous_variant | 3/5 | ||
UBE2E1 | XM_005265431.6 | c.120C>T | p.Gly40= | synonymous_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2E1 | ENST00000306627.8 | c.219C>T | p.Gly73= | synonymous_variant | 4/6 | 1 | NM_003341.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00565 AC: 860AN: 152130Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00556 AC: 1380AN: 247992Hom.: 7 AF XY: 0.00566 AC XY: 759AN XY: 134040
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GnomAD4 exome AF: 0.00964 AC: 14064AN: 1458828Hom.: 78 Cov.: 30 AF XY: 0.00935 AC XY: 6782AN XY: 725672
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GnomAD4 genome AF: 0.00564 AC: 859AN: 152248Hom.: 5 Cov.: 33 AF XY: 0.00517 AC XY: 385AN XY: 74426
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ClinVar
Significance: Benign/Likely 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 | clinical testing | Invitae | May 04, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | UBE2E1: BP4, BP7, BS2 - |
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