NM_016021.3:c.428+911C>T

Variant names:

• chr6-89337294-G-A
• rs1065657
• NM_016021.3:c.428+911C>T

Variant summary

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

The NM_016021.3(UBE2J1):​c.428+911C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 150,242 control chromosomes in the GnomAD database, including 25,382 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 0.56 (25382 hom., cov: 27)
• Consequence: UBE2J1 NM_016021.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2J1	NM_016021.3	c.428+911C>T		intron_variant	Intron 5 of 7	ENST00000435041.3	NP_057105.2
UBE2J1	XM_011535887.3	c.428+911C>T		intron_variant	Intron 5 of 6		XP_011534189.1
UBE2J1	XM_011535888.4	c.428+911C>T		intron_variant	Intron 5 of 7		XP_011534190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2J1	ENST00000435041.3	c.428+911C>T		intron_variant	Intron 5 of 7	1	NM_016021.3	ENSP00000451261.1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84028 AN: 150128 Hom.: 25321 Cov.: 27

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.560 AC: 84147 AN: 150242 Hom.: 25382 Cov.: 27 AF XY: 0.563 AC XY: 41146 AN XY: 73092

African (AFR) AF: 0.781 AC: 31999 AN: 40952

American (AMR) AF: 0.498 AC: 7514 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1765 AN: 3460

East Asian (EAS) AF: 0.721 AC: 3694 AN: 5124

South Asian (SAS) AF: 0.732 AC: 3495 AN: 4774

European-Finnish (FIN) AF: 0.415 AC: 4098 AN: 9874

Middle Eastern (MID) AF: 0.594 AC: 170 AN: 286

European-Non Finnish (NFE) AF: 0.440 AC: 29766 AN: 67692

Other (OTH) AF: 0.552 AC: 1150 AN: 2082

Alfa AF: 0.470 Hom.: 15726

Bravo AF: 0.571

Asia WGS AF: 0.736 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.24
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: rs1065657; hg19: chr6-90047013;