dbSNP rs12144146: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2Q1	NM_017582.7 link	c.815-33T>C		intron_variant	Intron 6 of 12	ENST00000292211.5	NP_060052.3	Q7Z7E8-1
UBE2Q1	XM_047424467.1 link	c.815-33T>C		intron_variant	Intron 6 of 11		XP_047280423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2Q1	ENST00000292211.5 link	c.815-33T>C		intron_variant	Intron 6 of 12	1	NM_017582.7	ENSP00000292211.4		Q7Z7E8-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over