rs16951415

Variant names:

• chr13-96004933-T-C
• rs16951415
• NM_020121.4:c.661-5626A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020121.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT2	NM_020121.4	MANE Select	c.661-5626A>G		intron	N/A	NP_064506.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT2	ENST00000376747.8	TSL:1 MANE Select	c.661-5626A>G		intron	N/A	ENSP00000365938.3
	UGGT2	ENST00000397618.7	TSL:1	c.661-5626A>G		intron	N/A	ENSP00000380743.3
	UGGT2	ENST00000376712.4	TSL:1	c.661-5626A>G		intron	N/A	ENSP00000365902.4

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

African (AFR) AF: 0.137 AC: 5687 AN: 41364

American (AMR) AF: 0.138 AC: 2113 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3464

East Asian (EAS) AF: 0.0612 AC: 315 AN: 5146

South Asian (SAS) AF: 0.0904 AC: 435 AN: 4814

European-Finnish (FIN) AF: 0.183 AC: 1921 AN: 10506

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10762 AN: 67932

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.157 Hom.: 1179

Bravo AF: 0.146

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16951415; hg19: chr13-96657187;