Variant 11-119096581-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBA1

The NM_001382.4(DPAGT1):c.*417T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 306,606 control chromosomes in the GnomAD database, including 16,986 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7701 hom., cov: 32)

Exomes 𝑓: 0.33 ( 9285 hom. )

Consequence

DPAGT1
NM_001382.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.51

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.16).

BP6

Variant 11-119096581-A-G is Benign according to our data. Variant chr11-119096581-A-G is described in ClinVar as [Benign]. Clinvar id is 302741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPAGT1	NM_001382.4 linkuse as main transcript	c.*417T>C		3_prime_UTR_variant	9/9	ENST00000354202.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPAGT1	ENST00000354202.9 linkuse as main transcript	c.*417T>C		3_prime_UTR_variant	9/9	1	NM_001382.4	P1	Q9H3H5-1

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45680

AN:

151944

Hom.:

7695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.331

GnomAD4 exome

AF:

0.330

AC:

50969

AN:

154544

Hom.:

9285

Cov.:

AF XY:

0.319

AC XY:

26482

AN XY:

82888

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.248

Gnomad4 ASJ exome

AF:

0.447

Gnomad4 EAS exome

AF:

0.486

Gnomad4 SAS exome

AF:

0.198

Gnomad4 FIN exome

AF:

0.353

Gnomad4 NFE exome

AF:

0.359

Gnomad4 OTH exome

AF:

0.346

GnomAD4 genome

AF:

0.301

AC:

45707

AN:

152062

Hom.:

7701

Cov.:

AF XY:

0.300

AC XY:

22282

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.450

Gnomad4 EAS

AF:

0.498

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.375

Gnomad4 NFE

AF:

0.370

Gnomad4 OTH

AF:

0.333

Alfa

AF:

0.356

Hom.:

9614

Bravo

AF:

0.290

Asia WGS

AF:

0.305

AC:

1063

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Acute intermittent porphyria

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

DPAGT1-congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.16

Cadd

Benign

Dann

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over