Variant 11-119102402-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000409993.6(DPAGT1):c.-367-54T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 457,366 control chromosomes in the GnomAD database, including 203,239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.96 ( 70115 hom., cov: 32)

Exomes 𝑓: 0.93 ( 133124 hom. )

Consequence

DPAGT1
ENST00000409993.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0220

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:

C2CD2L (HGNC:29000): (C2CD2 like) Enables phosphatidylinositol binding activity and phosphatidylinositol transfer activity. Involved in positive regulation of insulin secretion involved in cellular response to glucose stimulus. Located in cortical endoplasmic reticulum and endoplasmic reticulum-plasma membrane contact site. Colocalizes with cytoplasmic side of apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

C2CD2L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BP6

Variant 11-119102402-A-G is Benign according to our data. Variant chr11-119102402-A-G is described in ClinVar as [Benign]. Clinvar id is 680555.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2CD2L	XM_047427937.1 link	c.-424+27A>G		intron_variant			XP_047283893.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
DPAGT1	ENST00000409993.6 link	c.-367-54T>C	intron_variant	2	ENSP00000386597.2	Q9H3H5-1
C2CD2L	ENST00000534024.1 link	n.178+27A>G	intron_variant	4
DPAGT1	ENST00000442480.1 link	n.-31T>C	upstream_gene_variant	5	ENSP00000406591.1	H7C2L6

Frequencies

GnomAD3 genomes

AF:

0.959

AC:

145796

AN:

152048

Hom.:

70056

Cov.:

show subpopulations

Gnomad AFR

AF:

0.984

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.965

Gnomad ASJ

AF:

0.987

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.818

Gnomad FIN

AF:

0.894

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.971

Gnomad OTH

AF:

0.968

GnomAD3 exomes

AF:

0.926

AC:

127806

AN:

137964

Hom.:

59555

AF XY:

0.920

AC XY:

68649

AN XY:

74616

show subpopulations

Gnomad AFR exome

AF:

0.981

Gnomad AMR exome

AF:

0.960

Gnomad ASJ exome

AF:

0.987

Gnomad EAS exome

AF:

0.805

Gnomad SAS exome

AF:

0.824

Gnomad FIN exome

AF:

0.890

Gnomad NFE exome

AF:

0.972

Gnomad OTH exome

AF:

0.953

GnomAD4 exome

AF:

0.931

AC:

284235

AN:

305200

Hom.:

133124

Cov.:

AF XY:

0.921

AC XY:

158387

AN XY:

171918

show subpopulations

Gnomad4 AFR exome

AF:

0.982

Gnomad4 AMR exome

AF:

0.960

Gnomad4 ASJ exome

AF:

0.988

Gnomad4 EAS exome

AF:

0.807

Gnomad4 SAS exome

AF:

0.827

Gnomad4 FIN exome

AF:

0.893

Gnomad4 NFE exome

AF:

0.972

Gnomad4 OTH exome

AF:

0.949

GnomAD4 genome

AF:

0.959

AC:

145911

AN:

152166

Hom.:

70115

Cov.:

AF XY:

0.952

AC XY:

70767

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.984

Gnomad4 AMR

AF:

0.965

Gnomad4 ASJ

AF:

0.987

Gnomad4 EAS

AF:

0.809

Gnomad4 SAS

AF:

0.818

Gnomad4 FIN

AF:

0.894

Gnomad4 NFE

AF:

0.971

Gnomad4 OTH

AF:

0.969

Alfa

AF:

0.972

Hom.:

18425

Bravo

AF:

0.967

Asia WGS

AF:

0.810

AC:

2819

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-1.1

CADD

Benign

7.8

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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