Variant chr20-50082386-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000371674.8(UBE2V1):c.*382C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 192,996 control chromosomes in the GnomAD database, including 11,781 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 0.35 ( 10301 hom., cov: 31)

Exomes 𝑓: 0.25 ( 1480 hom. )

Consequence

UBE2V1
ENST00000371674.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.763

Variant links:

Genes affected

UBE2V1 (HGNC:12494): (ubiquitin conjugating enzyme E2 V1) Ubiquitin-conjugating E2 enzyme variant proteins constitute a distinct subfamily within the E2 protein family. They have sequence similarity to other ubiquitin-conjugating enzymes but lack the conserved cysteine residue that is critical for the catalytic activity of E2s. The protein encoded by this gene is located in the nucleus and can cause transcriptional activation of the human FOS proto-oncogene. It is thought to be involved in the control of differentiation by altering cell cycle behavior. Alternatively spliced transcript variants encoding multiple isoforms have been described for this gene, and multiple pseudogenes of this gene have been identified. Co-transcription of this gene and the neighboring upstream gene generates a rare transcript (Kua-UEV), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Apr 2012]

UBE2V1 links:

PEDS1-UBE2V1 (HGNC:):

PEDS1-UBE2V1 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2V1	NM_001032288.3 linkuse as main transcript	c.*382C>T		3_prime_UTR_variant	4/4	ENST00000371674.8	NP_001027459.1
PEDS1-UBE2V1	NM_199203.3 linkuse as main transcript	c.*382C>T		3_prime_UTR_variant	8/8		NP_954673.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2V1	ENST00000371674.8 linkuse as main transcript	c.*382C>T		3_prime_UTR_variant	4/4	1	NM_001032288.3	ENSP00000360739	P1	Q13404-4

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52639

AN:

151772

Hom.:

10277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.332

GnomAD4 exome

AF:

0.250

AC:

10261

AN:

41106

Hom.:

1480

Cov.:

AF XY:

0.259

AC XY:

5877

AN XY:

22698

show subpopulations

Gnomad4 AFR exome

AF:

0.490

Gnomad4 AMR exome

AF:

0.253

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.324

Gnomad4 FIN exome

AF:

0.233

Gnomad4 NFE exome

AF:

0.225

Gnomad4 OTH exome

AF:

0.275

GnomAD4 genome

AF:

0.347

AC:

52707

AN:

151890

Hom.:

10301

Cov.:

AF XY:

0.345

AC XY:

25574

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.296

Gnomad4 ASJ

AF:

0.298

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.310

Hom.:

1015

Bravo

AF:

0.357

Asia WGS

AF:

0.337

AC:

1168

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.6

DANN

Benign

0.53

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