rs10510536

Variant names:

• chr3-23228279-T-C
• rs10510536
• NM_152653.4:c.227+10967T>C

Variant summary

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

The NM_152653.4(UBE2E2):​c.227+10967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,102 control chromosomes in the GnomAD database, including 2,344 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 0.16 (2344 hom., cov: 32)
• Consequence: UBE2E2 NM_152653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2E2	NM_152653.4	c.227+10967T>C		intron_variant	Intron 3 of 5	ENST00000396703.6	NP_689866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2E2	ENST00000396703.6	c.227+10967T>C		intron_variant	Intron 3 of 5	1	NM_152653.4	ENSP00000379931.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24775 AN: 151984 Hom.: 2342 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.163 AC: 24795 AN: 152102 Hom.: 2344 Cov.: 32 AF XY: 0.166 AC XY: 12380 AN XY: 74364

African (AFR) AF: 0.255 AC: 10564 AN: 41480

American (AMR) AF: 0.104 AC: 1584 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3472

East Asian (EAS) AF: 0.190 AC: 987 AN: 5184

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1974 AN: 10552

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7704 AN: 67996

Other (OTH) AF: 0.148 AC: 314 AN: 2116

Alfa AF: 0.133 Hom.: 374

Bravo AF: 0.160

Asia WGS AF: 0.244 AC: 843 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.54
PhyloP100		0.016
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: rs10510536; hg19: chr3-23269770;