rs11903649

chr2-128133493-C-T

Variant summary

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

The NM_020120.4(UGGT1):c.1497+233C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,972 control chromosomes in the GnomAD database, including 14,041 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 0.42 (14041 hom., cov: 32)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGGT1	NM_020120.4	c.1497+233C>T		intron_variant		ENST00000259253.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT1	ENST00000259253.11	c.1497+233C>T		intron_variant		1	NM_020120.4	P1
UGGT1	ENST00000376723.7	c.*1537+233C>T		intron_variant, NMD_transcript_variant		1
UGGT1	ENST00000438277.5	c.*1085+233C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64519 AN: 151854 Hom.: 14036 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.425 AC: 64550 AN: 151972 Hom.: 14041 Cov.: 32 AF XY: 0.426 AC XY: 31623 AN XY: 74262

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.451

Alfa AF: 0.419 Hom.: 13619

Bravo AF: 0.440

Asia WGS AF: 0.417 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.41

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: rs11903649; hg19: chr2-128891067; COSMIC: COSV52141456;