6-89346362-G-T

Variant names:

• chr6-89346362-G-T
• rs7743444
• NM_016021.3:c.32-2606C>A

Variant summary

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

The NM_016021.3(UBE2J1):​c.32-2606C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,874 control chromosomes in the GnomAD database, including 9,157 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 0.33 (9157 hom., cov: 31)
• Consequence: UBE2J1 NM_016021.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 7 publications found

Genes affected

UBE2J1 (HGNC:17598): (ubiquitin conjugating enzyme E2 J1) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is located in the membrane of the endoplasmic reticulum (ER) and may contribute to quality control ER-associated degradation by the ubiquitin-proteasome system. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2J1	NM_016021.3	c.32-2606C>A		intron_variant	Intron 1 of 7	ENST00000435041.3	NP_057105.2
UBE2J1	XM_011535887.3	c.32-2606C>A		intron_variant	Intron 1 of 6		XP_011534189.1
UBE2J1	XM_011535888.4	c.32-2606C>A		intron_variant	Intron 1 of 7		XP_011534190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2J1	ENST00000435041.3	c.32-2606C>A		intron_variant	Intron 1 of 7	1	NM_016021.3	ENSP00000451261.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49371 AN: 151756 Hom.: 9132 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.326 AC: 49454 AN: 151874 Hom.: 9157 Cov.: 31 AF XY: 0.331 AC XY: 24541 AN XY: 74232

African (AFR) AF: 0.470 AC: 19425 AN: 41368

American (AMR) AF: 0.321 AC: 4891 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3466

East Asian (EAS) AF: 0.583 AC: 3007 AN: 5160

South Asian (SAS) AF: 0.423 AC: 2039 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2872 AN: 10538

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15662 AN: 67946

Other (OTH) AF: 0.289 AC: 610 AN: 2108

Alfa AF: 0.260 Hom.: 25019

Bravo AF: 0.331

Asia WGS AF: 0.477 AC: 1659 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	1.4
DANN	Benign	0.60
PhyloP100		-0.18
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: rs7743444; hg19: chr6-90056081; COSMIC: COSV70562487;