2-128190321-T-C

Position:

• chr2-128190321-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.*579T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,114 control chromosomes in the GnomAD database, including 14,151 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 (14132 hom., cov: 31)
  • Exomes 𝑓: 0.44 (19 hom.)
• Consequence: UGGT1 NM_020120.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGGT1	NM_020120.4	c.*579T>C		3_prime_UTR_variant	41/41	ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.*579T>C		3_prime_UTR_variant	41/41	1	NM_020120.4	ENSP00000259253.6
UGGT1	ENST00000376723.7	n.*5287T>C		non_coding_transcript_exon_variant	41/41	1		ENSP00000365913.3
UGGT1	ENST00000376723.7	n.*5287T>C		3_prime_UTR_variant	41/41	1		ENSP00000365913.3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64963 AN: 151770 Hom.: 14125 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.442 AC: 100 AN: 226 Hom.: 19 Cov.: 0 AF XY: 0.410 AC XY: 55 AN XY: 134

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.286

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.450

Gnomad4 NFE exome AF: 0.466

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.428 AC: 65016 AN: 151888 Hom.: 14132 Cov.: 31 AF XY: 0.431 AC XY: 31963 AN XY: 74236

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.404

Alfa AF: 0.430 Hom.: 3386

Bravo AF: 0.416

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs9973651; hg19: chr2-128947895;