rs7986005

chr13-95947017-C-T

Variant summary

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

The NM_020121.4(UGGT2):c.1677+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,534,632 control chromosomes in the GnomAD database, including 126,929 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 0.40 (12266 hom., cov: 33)
  • Exomes 𝑓: 0.40 (114663 hom.)
• Consequence: UGGT2 NM_020121.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

Genes affected

UGGT2 (HGNC:15664): (UDP-glucose glycoprotein glucosyltransferase 2) 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGGT2	NM_020121.4	c.1677+20G>A		intron_variant		ENST00000376747.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT2	ENST00000376747.8	c.1677+20G>A		intron_variant		1	NM_020121.4	P1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60574 AN: 151866 Hom.: 12269 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.390

GnomAD3 exomes AF: 0.383 AC: 77765 AN: 202918 Hom.: 15536 AF XY: 0.388 AC XY: 42805 AN XY: 110452

Gnomad AFR exome AF: 0.398

Gnomad AMR exome AF: 0.210

Gnomad ASJ exome AF: 0.418

Gnomad EAS exome AF: 0.311

Gnomad SAS exome AF: 0.363

Gnomad FIN exome AF: 0.438

Gnomad NFE exome AF: 0.419

Gnomad OTH exome AF: 0.402

GnomAD4 exome AF: 0.405 AC: 559502 AN: 1382648 Hom.: 114663 Cov.: 30 AF XY: 0.405 AC XY: 276725 AN XY: 683522

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.224

Gnomad4 ASJ exome AF: 0.421

Gnomad4 EAS exome AF: 0.316

Gnomad4 SAS exome AF: 0.362

Gnomad4 FIN exome AF: 0.441

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.408

GnomAD4 genome AF: 0.399 AC: 60598 AN: 151984 Hom.: 12266 Cov.: 33 AF XY: 0.398 AC XY: 29533 AN XY: 74286

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.390

Alfa AF: 0.401 Hom.: 2640

Bravo AF: 0.384

Asia WGS AF: 0.336 AC: 1170 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.5
Dann	Benign	0.51
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: rs7986005; hg19: chr13-96599271; COSMIC: COSV65077780;