NM_017582.7:c.589-766G>C

Variant names:

• chr1-154553938-C-G
• rs7539745
• NM_017582.7:c.589-766G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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:40722): (UBE2Q1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017582.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2Q1	NM_017582.7	MANE Select	c.589-766G>C		intron	N/A	NP_060052.3
	UBE2Q1-AS1	NR_046668.1		n.64+266C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2Q1	ENST00000292211.5	TSL:1 MANE Select	c.589-766G>C		intron	N/A	ENSP00000292211.4	Q7Z7E8-1
	UBE2Q1	ENST00000971180.1		c.589-766G>C		intron	N/A	ENSP00000641239.1
	UBE2Q1	ENST00000926346.1		c.589-766G>C		intron	N/A	ENSP00000596405.1

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

African (AFR) AF: 0.677 AC: 28046 AN: 41454

American (AMR) AF: 0.827 AC: 12650 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4628 AN: 5180

South Asian (SAS) AF: 0.821 AC: 3961 AN: 4822

European-Finnish (FIN) AF: 0.844 AC: 8950 AN: 10604

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56745 AN: 68002

Other (OTH) AF: 0.820 AC: 1735 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.37
PhyloP100		0.088
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: rs7539745; hg19: chr1-154526414;