chr11-119105217-A-G

Position:

• chr11-119105217-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

C2CD2L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2CD2L	XM_047427937.1	c.-423-1854A>G		intron_variant			XP_047283893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPAGT1	ENST00000409993.6	c.-368+1930T>C		intron_variant		2		ENSP00000386597.2
C2CD2L	ENST00000534024.1	n.179-2158A>G		intron_variant		4

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

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.935

Alfa AF: 0.942 Hom.: 68835

Bravo AF: 0.935

Asia WGS AF: 0.744 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.82

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: rs10790283; hg19: chr11-118975927;