NM_016021.3:c.31+3589G>A

Variant names:

• chr6-89348950-C-T
• rs9351207
• NM_016021.3:c.31+3589G>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.31+3589G>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 152,008 control chromosomes in the GnomAD database, including 9,198 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 (9198 hom., cov: 32)
• Consequence: UBE2J1 NM_016021.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2J1	NM_016021.3	c.31+3589G>A		intron_variant	Intron 1 of 7	ENST00000435041.3	NP_057105.2
UBE2J1	XM_011535887.3	c.31+3589G>A		intron_variant	Intron 1 of 6		XP_011534189.1
UBE2J1	XM_011535888.4	c.31+3589G>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.31+3589G>A		intron_variant	Intron 1 of 7	1	NM_016021.3	ENSP00000451261.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49400 AN: 151890 Hom.: 9174 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.229

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: 49482 AN: 152008 Hom.: 9198 Cov.: 32 AF XY: 0.331 AC XY: 24571 AN XY: 74298

African (AFR) AF: 0.471 AC: 19501 AN: 41434

American (AMR) AF: 0.319 AC: 4881 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3065 AN: 5170

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2913 AN: 10554

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

European-Non Finnish (NFE) AF: 0.229 AC: 15536 AN: 67960

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.262 Hom.: 2966

Bravo AF: 0.331

Asia WGS AF: 0.477 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.31
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: rs9351207; hg19: chr6-90058669; COSMIC: COSV70562494;