rs1496653
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152653.4(UBE2E2):c.228-86309A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,038 control chromosomes in the GnomAD database, including 5,303 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5303 hom., cov: 32)
Consequence
UBE2E2
NM_152653.4 intron
NM_152653.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.594
Genes affected
UBE2E2 (HGNC:12478): (ubiquitin conjugating enzyme E2 E2) Enables ISG15 transferase activity and ubiquitin conjugating enzyme activity. Involved in protein modification by small protein conjugation. Acts upstream of or within cellular response to DNA damage stimulus and positive regulation of G1/S transition of mitotic cell cycle. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE2E2 | NM_152653.4 | c.228-86309A>G | intron_variant | ENST00000396703.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2E2 | ENST00000396703.6 | c.228-86309A>G | intron_variant | 1 | NM_152653.4 | P1 | |||
UBE2E2 | ENST00000335798.8 | c.228-119255A>G | intron_variant, NMD_transcript_variant | 1 | |||||
UBE2E2 | ENST00000425792.5 | c.228-86309A>G | intron_variant | 2 | P1 | ||||
UBE2E2 | ENST00000452894.5 | c.300-86309A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.252 AC: 38343AN: 151920Hom.: 5291 Cov.: 32
GnomAD3 genomes
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151920
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.253 AC: 38390AN: 152038Hom.: 5303 Cov.: 32 AF XY: 0.256 AC XY: 19004AN XY: 74286
GnomAD4 genome
?
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38390
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32
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19004
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74286
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Asia WGS
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847
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at