2-128192319-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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 rank	MANE	Protein	UniProt
UGGT1	NM_020120.4	c.*2577A>G		3_prime_UTR_variant	Exon 41 of 41	ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.*2577A>G		3_prime_UTR_variant	Exon 41 of 41	1	NM_020120.4	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

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

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.406

Alfa AF: 0.425 Hom.: 2123

Bravo AF: 0.419

Asia WGS AF: 0.513 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.053
DANN	Benign	0.37
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: rs1054317; hg19: chr2-128949893;