NM_152653.4:c.228-42607G>A

Variant names:

• chr3-23457001-G-A
• rs778480
• NM_152653.4:c.228-42607G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152653.4(UBE2E2):​c.228-42607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,116 control chromosomes in the GnomAD database, including 36,229 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 0.67 (36229 hom., cov: 32)
• Consequence: UBE2E2 NM_152653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2E2	NM_152653.4	c.228-42607G>A		intron_variant	Intron 3 of 5	ENST00000396703.6	NP_689866.1
UBE2E2	NM_001370225.1	c.228-42607G>A		intron_variant	Intron 3 of 5		NP_001357154.1
UBE2E2	NM_001370226.1	c.228-42607G>A		intron_variant	Intron 3 of 5		NP_001357155.1
UBE2E2	XM_047448843.1	c.228-42607G>A		intron_variant	Intron 3 of 5		XP_047304799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2E2	ENST00000396703.6	c.228-42607G>A		intron_variant	Intron 3 of 5	1	NM_152653.4	ENSP00000379931.1
UBE2E2	ENST00000335798.8	n.228-75553G>A		intron_variant	Intron 3 of 4	1		ENSP00000338340.4
UBE2E2	ENST00000425792.5	c.228-42607G>A		intron_variant	Intron 3 of 5	2		ENSP00000401053.1
UBE2E2	ENST00000452894.5	c.300-42607G>A		intron_variant	Intron 4 of 5	3		ENSP00000392800.1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 102011 AN: 151998 Hom.: 36180 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.652

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.671 AC: 102112 AN: 152116 Hom.: 36229 Cov.: 32 AF XY: 0.669 AC XY: 49718 AN XY: 74354

African (AFR) AF: 0.915 AC: 37993 AN: 41542

American (AMR) AF: 0.495 AC: 7562 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2062 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3808 AN: 5170

South Asian (SAS) AF: 0.639 AC: 3077 AN: 4814

European-Finnish (FIN) AF: 0.641 AC: 6771 AN: 10570

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38949 AN: 67956

Other (OTH) AF: 0.649 AC: 1371 AN: 2114

Alfa AF: 0.635 Hom.: 4669

Bravo AF: 0.672

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.26
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs778480; hg19: chr3-23498492;