rs6795968

Variant names:

• chr3-23375536-A-C
• rs6795968
• NM_152653.4:c.228-124072A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-23375536-A-C
• chr3-23375536-A-T

Variant summary

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

The NM_152653.4(UBE2E2):​c.228-124072A>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 NM_152653.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 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=-0.92).
• 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 rank	MANE	Protein	UniProt
UBE2E2	NM_152653.4	c.228-124072A>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.228-124072A>C		intron_variant	Intron 3 of 5	1	NM_152653.4	ENSP00000379931.1
UBE2E2	ENST00000335798.8	n.228-157018A>C		intron_variant	Intron 3 of 4	1		ENSP00000338340.4
UBE2E2	ENST00000425792.5	c.228-124072A>C		intron_variant	Intron 3 of 5	2		ENSP00000401053.1
UBE2E2	ENST00000452894.5	c.299+51950A>C		intron_variant	Intron 4 of 5	3		ENSP00000392800.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82790 AN: 151824 Hom.: 22785 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.545 AC: 82880 AN: 151942 Hom.: 22823 Cov.: 32 AF XY: 0.545 AC XY: 40484 AN XY: 74246

African (AFR) AF: 0.530 AC: 21960 AN: 41446

American (AMR) AF: 0.656 AC: 10006 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2485 AN: 5174

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4812

European-Finnish (FIN) AF: 0.532 AC: 5616 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37291 AN: 67918

Other (OTH) AF: 0.549 AC: 1159 AN: 2112

Alfa AF: 0.553 Hom.: 3241

Bravo AF: 0.557

Asia WGS AF: 0.497 AC: 1727 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.43
PhyloP100		-1.1
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: rs6795968; hg19: chr3-23417027;