Genetic Variant UBE2Q1:c.815-33T>C (chr1-154552497-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017582.7(UBE2Q1):c.815-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,613,124 control chromosomes in the GnomAD database, including 66,534 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 0.21 ( 4516 hom., cov: 33)

Exomes 𝑓: 0.28 ( 62018 hom. )

Consequence

UBE2Q1
NM_017582.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19

Publications

10 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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.815-33T>C		intron	N/A	NP_060052.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBE2Q1	ENST00000292211.5	TSL:1 MANE Select	c.815-33T>C	intron	N/A	ENSP00000292211.4	Q7Z7E8-1
UBE2Q1	ENST00000971180.1		c.812-33T>C	intron	N/A	ENSP00000641239.1
UBE2Q1	ENST00000926346.1		c.815-33T>C	intron	N/A	ENSP00000596405.1

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32526

AN:

152148

Hom.:

4518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0554

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.0146

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.228

GnomAD2 exomes

AF:

0.234

AC:

58756

AN:

250864

AF XY:

0.237

show subpopulations

Gnomad AFR exome

AF:

0.0487

Gnomad AMR exome

AF:

0.244

Gnomad ASJ exome

AF:

0.245

Gnomad EAS exome

AF:

0.00647

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.303

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.281

AC:

411025

AN:

1460858

Hom.:

62018

Cov.:

AF XY:

0.278

AC XY:

202327

AN XY:

726692

show subpopulations

African (AFR)

AF:

0.0476

AC:

1592

AN:

33464

American (AMR)

AF:

0.245

AC:

10949

AN:

44668

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

6515

AN:

26096

East Asian (EAS)

AF:

0.0225

AC:

895

AN:

39694

South Asian (SAS)

AF:

0.152

AC:

13127

AN:

86146

European-Finnish (FIN)

AF:

0.288

AC:

15355

AN:

53404

Middle Eastern (MID)

AF:

0.208

AC:

1201

AN:

5766

European-Non Finnish (NFE)

AF:

0.312

AC:

346272

AN:

1111258

Other (OTH)

AF:

0.250

AC:

15119

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

15934

31867

47801

63734

79668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11064

22128

33192

44256

55320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.214

AC:

32523

AN:

152266

Hom.:

4516

Cov.:

AF XY:

0.211

AC XY:

15682

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0553

AC:

2297

AN:

41566

American (AMR)

AF:

0.256

AC:

3916

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

886

AN:

3468

East Asian (EAS)

AF:

0.0146

AC:

AN:

5194

South Asian (SAS)

AF:

0.141

AC:

679

AN:

4822

European-Finnish (FIN)

AF:

0.291

AC:

3085

AN:

10606

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20688

AN:

67998

Other (OTH)

AF:

0.225

AC:

475

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1246

2492

3737

4983

6229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.262

Hom.:

1768

Bravo

AF:

0.205

Asia WGS

AF:

0.0720

AC:

256

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.1

(source)

DANN

Benign

0.59

PhyloP100

1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over