2-128158852-G-C

Position:

• chr2-128158852-G-C

Variant summary

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

The NM_020120.4(UGGT1):​c.2356-662G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,940 control chromosomes in the GnomAD database, including 14,302 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 (14302 hom., cov: 32)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-0.98).
• 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	UniProt
UGGT1	NM_020120.4	c.2356-662G>C		intron_variant		ENST00000259253.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT1	ENST00000259253.11	c.2356-662G>C		intron_variant		1	NM_020120.4	P1
UGGT1	ENST00000376723.7	c.*2396-662G>C		intron_variant, NMD_transcript_variant		1
UGGT1	ENST00000438277.5	c.*1944-662G>C		intron_variant, NMD_transcript_variant		1
UGGT1	ENST00000488439.1	n.632-662G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65439 AN: 151822 Hom.: 14292 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.431 AC: 65500 AN: 151940 Hom.: 14302 Cov.: 32 AF XY: 0.434 AC XY: 32199 AN XY: 74240

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.415

Alfa AF: 0.422 Hom.: 1664

Bravo AF: 0.419

Asia WGS AF: 0.515 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.69

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: rs13405489; hg19: chr2-128916426;