rs6546038

Positions:

• chr2-63889455-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006759.4(UGP2):​c.1315-626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,036 control chromosomes in the GnomAD database, including 46,513 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 0.77 (46485 hom., cov: 29)
  • Exomes 𝑓: 0.76 (28 hom.)
• Consequence: UGP2 NM_006759.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGP2	NM_006759.4	c.1315-626G>A		intron_variant		ENST00000337130.10	NP_006750.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGP2	ENST00000337130.10	c.1315-626G>A		intron_variant		1	NM_006759.4	ENSP00000338703.5

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116951 AN: 151824 Hom.: 46442 Cov.: 29

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.755 AC: 71 AN: 94 Hom.: 28 Cov.: 0 AF XY: 0.727 AC XY: 48 AN XY: 66

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.811

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.770 AC: 117052 AN: 151942 Hom.: 46485 Cov.: 29 AF XY: 0.765 AC XY: 56789 AN XY: 74242

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.755

Alfa AF: 0.765 Hom.: 44017

Bravo AF: 0.767

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.73
DANN	Benign	0.79

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

Other links and lift over

dbSNP: rs6546038; hg19: chr2-64116589;