chr3-23294959-C-A

Variant names:

• chr3-23294959-C-A
• rs7612463
• NM_152653.4:c.227+77647C>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.227+77647C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,928 control chromosomes in the GnomAD database, including 1,813 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 0.15 (1813 hom., cov: 32)
• Consequence: UBE2E2 NM_152653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 72 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152653.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2E2	NM_152653.4	MANE Select	c.227+77647C>A		intron	N/A	NP_689866.1
	UBE2E2	NM_001370225.1		c.227+77647C>A		intron	N/A	NP_001357154.1
	UBE2E2	NM_001370226.1		c.227+77647C>A		intron	N/A	NP_001357155.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2E2	ENST00000396703.6	TSL:1 MANE Select	c.227+77647C>A		intron	N/A	ENSP00000379931.1
	UBE2E2	ENST00000335798.8	TSL:1	n.227+77647C>A		intron	N/A	ENSP00000338340.4
	UBE2E2	ENST00000425792.5	TSL:2	c.227+77647C>A		intron	N/A	ENSP00000401053.1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22518 AN: 151812 Hom.: 1811 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.148 AC: 22536 AN: 151928 Hom.: 1813 Cov.: 32 AF XY: 0.152 AC XY: 11293 AN XY: 74232

African (AFR) AF: 0.206 AC: 8532 AN: 41420

American (AMR) AF: 0.0954 AC: 1457 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.190 AC: 980 AN: 5164

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 1996 AN: 10502

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7746 AN: 67970

Other (OTH) AF: 0.136 AC: 288 AN: 2110

Alfa AF: 0.122 Hom.: 5404

Bravo AF: 0.143

Asia WGS AF: 0.226 AC: 787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		-0.050
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: rs7612463; hg19: chr3-23336450;