6-89327862-G-A

Position:

• chr6-89327862-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435041.3(UBE2J1):​c.*1817C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,176 control chromosomes in the GnomAD database, including 1,815 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 0.14 (1815 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBE2J1 ENST00000435041.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2J1	NM_016021.3	c.*1817C>T		3_prime_UTR_variant	8/8	ENST00000435041.3	NP_057105.2
UBE2J1	XM_011535887.3	c.*1817C>T		3_prime_UTR_variant	7/7		XP_011534189.1
UBE2J1	XM_011535888.4	c.*2096C>T		3_prime_UTR_variant	8/8		XP_011534190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2J1	ENST00000435041.3	c.*1817C>T		3_prime_UTR_variant	8/8	1	NM_016021.3	ENSP00000451261	P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21684 AN: 152058 Hom.: 1814 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.162

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.142 AC: 21685 AN: 152176 Hom.: 1815 Cov.: 32 AF XY: 0.145 AC XY: 10790 AN XY: 74394

Gnomad4 AFR AF: 0.0691

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.168

Alfa AF: 0.174 Hom.: 2842

Bravo AF: 0.133

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.51

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: rs9048; hg19: chr6-90037581;