rs6795968
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000396703.6(UBE2E2):c.228-124072A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,942 control chromosomes in the GnomAD database, including 22,823 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 0.55 ( 22823 hom., cov: 32)
Consequence
UBE2E2
ENST00000396703.6 intron
ENST00000396703.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBE2E2 | NM_152653.4 | c.228-124072A>C | intron_variant | ENST00000396703.6 | NP_689866.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBE2E2 | ENST00000396703.6 | c.228-124072A>C | intron_variant | 1 | NM_152653.4 | ENSP00000379931 | P1 | |||
UBE2E2 | ENST00000335798.8 | c.228-157018A>C | intron_variant, NMD_transcript_variant | 1 | ENSP00000338340 | |||||
UBE2E2 | ENST00000425792.5 | c.228-124072A>C | intron_variant | 2 | ENSP00000401053 | P1 | ||||
UBE2E2 | ENST00000452894.5 | c.299+51950A>C | intron_variant | 3 | ENSP00000392800 |
Frequencies
GnomAD3 genomes AF: 0.545 AC: 82790AN: 151824Hom.: 22785 Cov.: 32
GnomAD3 genomes
AF:
AC:
82790
AN:
151824
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.545 AC: 82880AN: 151942Hom.: 22823 Cov.: 32 AF XY: 0.545 AC XY: 40484AN XY: 74246
GnomAD4 genome
AF:
AC:
82880
AN:
151942
Hom.:
Cov.:
32
AF XY:
AC XY:
40484
AN XY:
74246
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1727
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at