11-119095811-C-T

Variant names:

• chr11-119095811-C-T
• rs2509049
• XM_047426508.1:c.*1187G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XM_047426508.1(DPAGT1):​c.*1187G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,744 control chromosomes in the GnomAD database, including 11,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (11878 hom., cov: 31)
• Consequence: DPAGT1 XM_047426508.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.18
• Publications: 20 publications found

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]

DPAGT1 Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 13

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P
• DPAGT1-congenital disorder of glycosylation

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, ClinGen
• congenital myasthenic syndromes with glycosylation defect

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 11-119095811-C-T is Benign according to our data. Variant chr11-119095811-C-T is described in ClinVar as Benign. ClinVar VariationId is 1296893.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000682232.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPAGT1	ENST00000682232.1		n.*2031G>A		downstream_gene	N/A	ENSP00000507302.1	F8W681

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58510 AN: 151626 Hom.: 11866 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.386 AC: 58547 AN: 151744 Hom.: 11878 Cov.: 31 AF XY: 0.388 AC XY: 28750 AN XY: 74144

African (AFR) AF: 0.289 AC: 11943 AN: 41352

American (AMR) AF: 0.326 AC: 4979 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3273 AN: 5152

South Asian (SAS) AF: 0.489 AC: 2348 AN: 4806

European-Finnish (FIN) AF: 0.392 AC: 4120 AN: 10508

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28575 AN: 67888

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.405 Hom.: 15889

Bravo AF: 0.376

Asia WGS AF: 0.521 AC: 1814 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.45
DANN	Benign	0.76
PhyloP100		-1.2
PromoterAI		0.018	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2509049; hg19: chr11-118966521;