2-128093088-C-A

Position:

• chr2-128093088-C-A

Variant summary

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

The NM_020120.4(UGGT1):​c.58+1673C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,988 control chromosomes in the GnomAD database, including 25,657 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 0.58 (25657 hom., cov: 32)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

UGGT1 (HGNC:15663): (UDP-glucose glycoprotein glucosyltransferase 1) UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER.[supplied by OMIM, Oct 2009]

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 (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGGT1	NM_020120.4	c.58+1673C>A		intron_variant		ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.58+1673C>A		intron_variant		1	NM_020120.4	ENSP00000259253	P1
UGGT1	ENST00000376723.7	c.*98+1492C>A		intron_variant, NMD_transcript_variant		1		ENSP00000365913
UGGT1	ENST00000438277.5	c.25+1706C>A		intron_variant, NMD_transcript_variant		1		ENSP00000392701
UGGT1	ENST00000430075.5	c.25+1706C>A		intron_variant, NMD_transcript_variant		4		ENSP00000400426

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87869 AN: 151872 Hom.: 25650 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.606

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.579 AC: 87927 AN: 151988 Hom.: 25657 Cov.: 32 AF XY: 0.576 AC XY: 42790 AN XY: 74276

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.600

Alfa AF: 0.545 Hom.: 8253

Bravo AF: 0.593

Asia WGS AF: 0.486 AC: 1687 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	5.2
DANN	Benign	0.59

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: rs11687190; hg19: chr2-128850662;