rs604714

chr11-119099986-C-Achr11-119099986-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001382.4(DPAGT1):c.643+276G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,698 control chromosomes in the GnomAD database, including 7,934 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.31 (7934 hom., cov: 30)
• Consequence: DPAGT1 NM_001382.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.236

Genes affected

DPAGT1 (HGNC:2995): (dolichyl-phosphate N-acetylglucosaminephosphotransferase 1) The protein encoded by this gene is an enzyme that catalyzes the first step in the dolichol-linked oligosaccharide pathway for glycoprotein biosynthesis. This enzyme belongs to the glycosyltransferase family 4. This protein is an integral membrane protein of the endoplasmic reticulum. The congenital disorder of glycosylation type Ij is caused by mutation in the gene encoding this enzyme. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 11-119099986-C-A is Benign according to our data. Variant chr11-119099986-C-A is described in ClinVar as [Benign]. Clinvar id is 680552.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPAGT1	NM_001382.4	c.643+276G>T		intron_variant		ENST00000354202.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPAGT1	ENST00000354202.9	c.643+276G>T		intron_variant		1	NM_001382.4	P1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47235 AN: 151580 Hom.: 7933 Cov.: 30

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.311 AC: 47251 AN: 151698 Hom.: 7934 Cov.: 30 AF XY: 0.311 AC XY: 23040 AN XY: 74114

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.341

Alfa AF: 0.323 Hom.: 1312

Bravo AF: 0.303

Asia WGS AF: 0.300 AC: 1049 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.8
Dann	Benign	0.62

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: rs604714; hg19: chr11-118970696;