Variant rs12144146 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
UBE2Q1	NM_017582.7 linkuse as main transcript	c.815-33T>C		intron_variant		ENST00000292211.5	NP_060052.3
UBE2Q1	XM_047424467.1 linkuse as main transcript	c.815-33T>C		intron_variant			XP_047280423.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2Q1	ENST00000292211.5 linkuse as main transcript	c.815-33T>C	intron_variant		1	NM_017582.7	ENSP00000292211	P1	Q7Z7E8-1
UBE2Q1	ENST00000483639.1 linkuse as main transcript	n.369T>C	non_coding_transcript_exon_variant	2/6	3
UBE2Q1	ENST00000467683.5 linkuse as main transcript	n.86-33T>C	intron_variant, non_coding_transcript_variant		5
UBE2Q1	ENST00000497453.1 linkuse as main transcript	n.748-33T>C	intron_variant, non_coding_transcript_variant		5

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

GnomAD3 exomes

AF:

0.234

AC:

58756

AN:

250864

Hom.:

8219

AF XY:

0.237

AC XY:

32166

AN XY:

135542

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 SAS exome

AF:

0.149

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

Gnomad4 AFR exome

AF:

0.0476

Gnomad4 AMR exome

AF:

0.245

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.0225

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.288

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.214

AC:

32523

AN:

152266

Hom.:

4516

Cov.:

AF XY:

0.211

AC XY:

15682

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0553

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.0146

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.225

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

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over