rs7539745

Positions:

• chr1-154553938-C-G
• chr1-154553938-C-T

Variant summary

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

The NM_017582.7(UBE2Q1):​c.589-766G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,146 control chromosomes in the GnomAD database, including 48,136 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 0.79 (48136 hom., cov: 31)
• Consequence: UBE2Q1 NM_017582.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

UBE2Q1 (HGNC:15698): (ubiquitin conjugating enzyme E2 Q1) 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 (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin-protein ligases (E3s). This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. The encoded protein is 98% identical to the mouse counterpart. [provided by RefSeq, Jul 2008]

UBE2Q1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2Q1	NM_017582.7	c.589-766G>C		intron_variant		ENST00000292211.5	NP_060052.3
UBE2Q1	XM_047424467.1	c.589-766G>C		intron_variant			XP_047280423.1
UBE2Q1-AS1	NR_046668.1	n.64+266C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2Q1	ENST00000292211.5	c.589-766G>C		intron_variant		1	NM_017582.7	ENSP00000292211.4
UBE2Q1-AS1	ENST00000441613.1	n.64+266C>G		intron_variant		3
UBE2Q1	ENST00000497453.1	n.522-766G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120414 AN: 152028 Hom.: 48107 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.792 AC: 120494 AN: 152146 Hom.: 48136 Cov.: 31 AF XY: 0.794 AC XY: 59062 AN XY: 74398

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.820

Alfa AF: 0.808 Hom.: 6203

Bravo AF: 0.787

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.37

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: rs7539745; hg19: chr1-154526414;