Variant chr2-63857980-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006759.4(UGP2):c.255+44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 1,582,402 control chromosomes in the GnomAD database, including 533,109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 52337 hom., cov: 31)

Exomes 𝑓: 0.82 ( 480772 hom. )

Consequence

UGP2
NM_006759.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0370

Variant links:

Genes affected

UGP2 (HGNC:12527): (UDP-glucose pyrophosphorylase 2) The enzyme encoded by this gene is an important intermediary in mammalian carbohydrate interconversions. It transfers a glucose moiety from glucose-1-phosphate to MgUTP and forms UDP-glucose and MgPPi. In liver and muscle tissue, UDP-glucose is a direct precursor of glycogen; in lactating mammary gland it is converted to UDP-galactose which is then converted to lactose. The eukaryotic enzyme has no significant sequence similarity to the prokaryotic enzyme. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

UGP2 links:

UGP2 (HGNC:):

UGP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 2-63857980-G-A is Benign according to our data. Variant chr2-63857980-G-A is described in ClinVar as [Benign]. Clinvar id is 1684237.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGP2	NM_006759.4 linkuse as main transcript	c.255+44G>A		intron_variant		ENST00000337130.10	NP_006750.3	Q16851-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGP2	ENST00000337130.10 linkuse as main transcript	c.255+44G>A		intron_variant		1	NM_006759.4	ENSP00000338703.5		Q16851-1

Frequencies

GnomAD3 genomes

AF:

0.828

AC:

125901

AN:

151984

Hom.:

52275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.838

Gnomad AMI

AF:

0.910

Gnomad AMR

AF:

0.832

Gnomad ASJ

AF:

0.781

Gnomad EAS

AF:

0.913

Gnomad SAS

AF:

0.816

Gnomad FIN

AF:

0.876

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.821

GnomAD3 exomes

AF:

0.830

AC:

205051

AN:

246984

Hom.:

85352

AF XY:

0.827

AC XY:

110872

AN XY:

134062

show subpopulations

Gnomad AFR exome

AF:

0.834

Gnomad AMR exome

AF:

0.846

Gnomad ASJ exome

AF:

0.766

Gnomad EAS exome

AF:

0.912

Gnomad SAS exome

AF:

0.814

Gnomad FIN exome

AF:

0.880

Gnomad NFE exome

AF:

0.813

Gnomad OTH exome

AF:

0.812

GnomAD4 exome

AF:

0.819

AC:

1171731

AN:

1430300

Hom.:

480772

Cov.:

AF XY:

0.818

AC XY:

583314

AN XY:

713324

show subpopulations

Gnomad4 AFR exome

AF:

0.837

Gnomad4 AMR exome

AF:

0.842

Gnomad4 ASJ exome

AF:

0.764

Gnomad4 EAS exome

AF:

0.926

Gnomad4 SAS exome

AF:

0.812

Gnomad4 FIN exome

AF:

0.881

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.822

GnomAD4 genome

AF:

0.829

AC:

126022

AN:

152102

Hom.:

52337

Cov.:

AF XY:

0.830

AC XY:

61741

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.838

Gnomad4 AMR

AF:

0.832

Gnomad4 ASJ

AF:

0.781

Gnomad4 EAS

AF:

0.914

Gnomad4 SAS

AF:

0.815

Gnomad4 FIN

AF:

0.876

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.824

Alfa

AF:

0.795

Hom.:

6727

Bravo

AF:

0.827

Asia WGS

AF:

0.893

AC:

3104

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 83

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.6

DANN

Benign

0.48

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over