2-128135634-T-C

Position:

• chr2-128135634-T-C

Variant summary

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

The NM_020120.4(UGGT1):​c.1583+673T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,980 control chromosomes in the GnomAD database, including 14,497 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 0.43 (14497 hom., cov: 33)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

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]

UGGT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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	Protein	UniProt
UGGT1	NM_020120.4	c.1583+673T>C		intron_variant		ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.1583+673T>C		intron_variant		1	NM_020120.4	ENSP00000259253.6
UGGT1	ENST00000376723.7	n.*1623+673T>C		intron_variant		1		ENSP00000365913.3
UGGT1	ENST00000438277.5	n.*1171+673T>C		intron_variant		1		ENSP00000392701.1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65610 AN: 151862 Hom.: 14488 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.432 AC: 65655 AN: 151980 Hom.: 14497 Cov.: 33 AF XY: 0.433 AC XY: 32167 AN XY: 74298

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.456

Alfa AF: 0.412 Hom.: 7668

Bravo AF: 0.448

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.74
DANN	Benign	0.52

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: rs7577867; hg19: chr2-128893208;