rs16951415

Positions:

• chr13-96004933-T-C

Variant summary

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

The NM_020121.4(UGGT2):​c.661-5626A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,802 control chromosomes in the GnomAD database, including 1,800 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 0.15 (1800 hom., cov: 31)
• Consequence: UGGT2 NM_020121.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

Genes affected

UGGT2 (HGNC:15664): (UDP-glucose glycoprotein glucosyltransferase 2) 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGGT2	NM_020121.4	c.661-5626A>G		intron_variant		ENST00000376747.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT2	ENST00000376747.8	c.661-5626A>G		intron_variant		1	NM_020121.4	P1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22575 AN: 151684 Hom.: 1799 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.149 AC: 22581 AN: 151802 Hom.: 1800 Cov.: 31 AF XY: 0.149 AC XY: 11057 AN XY: 74182

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.0904

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.165

Alfa AF: 0.157 Hom.: 1076

Bravo AF: 0.146

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.76

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: rs16951415; hg19: chr13-96657187;