11-119105217-A-G

Variant names:

• chr11-119105217-A-G
• rs10790283
• ENST00000409993.6:c.-368+1930T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000409993.6(DPAGT1):​c.-368+1930T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,230 control chromosomes in the GnomAD database, including 65,827 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 0.93 (65827 hom., cov: 32)
• Consequence: DPAGT1 ENST00000409993.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 6 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]

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409993.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPAGT1	ENST00000409993.6	TSL:2	c.-368+1930T>C		intron	N/A	ENSP00000386597.2
	C2CD2L	ENST00000534024.1	TSL:4	n.179-2158A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141217 AN: 152114 Hom.: 65769 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.928 AC: 141331 AN: 152230 Hom.: 65827 Cov.: 32 AF XY: 0.922 AC XY: 68582 AN XY: 74410

African (AFR) AF: 0.944 AC: 39181 AN: 41518

American (AMR) AF: 0.945 AC: 14444 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3276 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3888 AN: 5170

South Asian (SAS) AF: 0.735 AC: 3545 AN: 4820

European-Finnish (FIN) AF: 0.888 AC: 9426 AN: 10610

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64414 AN: 68032

Other (OTH) AF: 0.935 AC: 1975 AN: 2112

Alfa AF: 0.943 Hom.: 109765

Bravo AF: 0.935

Asia WGS AF: 0.744 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10790283; hg19: chr11-118975927;