rs1065657

chr6-89337294-G-Achr6-89337294-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
UBE2J1	NM_016021.3	c.428+911C>T		intron_variant		ENST00000435041.3
UBE2J1	XM_011535887.3	c.428+911C>T		intron_variant
UBE2J1	XM_011535888.4	c.428+911C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2J1	ENST00000435041.3	c.428+911C>T		intron_variant		1	NM_016021.3	P1

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

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.552

Alfa AF: 0.473 Hom.: 11498

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1065657; hg19: chr6-90047013;