2-128192319-A-G

Variant names:

• chr2-128192319-A-G
• rs1054317
• NM_020120.4:c.*2577A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020120.4(UGGT1):​c.*2577A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 150,326 control chromosomes in the GnomAD database, including 14,072 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 (14072 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: UGGT1 NM_020120.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• disorder of protein N-glycosylation

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020120.4. 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
	UGGT1	NM_020120.4	MANE Select	c.*2577A>G		3_prime_UTR	Exon 41 of 41	NP_064505.1
	UGGT1	NR_027671.3		n.7584A>G		non_coding_transcript_exon	Exon 41 of 41

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.*2577A>G		3_prime_UTR	Exon 41 of 41	ENSP00000259253.6

Frequencies

GnomAD3 genomes AF: 0.430 AC: 64547 AN: 150220 Hom.: 14066 Cov.: 27

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.400

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.430 AC: 64592 AN: 150326 Hom.: 14072 Cov.: 27 AF XY: 0.432 AC XY: 31654 AN XY: 73282

African (AFR) AF: 0.435 AC: 17716 AN: 40732

American (AMR) AF: 0.361 AC: 5454 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1491 AN: 3464

East Asian (EAS) AF: 0.339 AC: 1735 AN: 5118

South Asian (SAS) AF: 0.574 AC: 2723 AN: 4748

European-Finnish (FIN) AF: 0.491 AC: 4970 AN: 10116

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29099 AN: 67758

Other (OTH) AF: 0.406 AC: 850 AN: 2094

Alfa AF: 0.429 Hom.: 3504

Bravo AF: 0.419

Asia WGS AF: 0.513 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.053
DANN	Benign	0.37
PhyloP100		-2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1054317; hg19: chr2-128949893;