chr11-119096070-A-C

Variant names:

• chr11-119096070-A-C
• rs2509851
• ENST00000682232.1:n.*1772T>G

Variant summary

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

The ENST00000682232.1(DPAGT1):​n.*1772T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,948 control chromosomes in the GnomAD database, including 7,740 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 0.30 (7740 hom., cov: 32)
• Consequence: DPAGT1 ENST00000682232.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• 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]

DPAGT1 Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 13

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

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

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPAGT1	XM_047426508.1	c.*928T>G		3_prime_UTR_variant	Exon 9 of 10		XP_047282464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPAGT1	ENST00000682232.1	n.*1772T>G		non_coding_transcript_exon_variant	Exon 7 of 7			ENSP00000507302.1
DPAGT1	ENST00000682232.1	n.*1772T>G		3_prime_UTR_variant	Exon 7 of 7			ENSP00000507302.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45704 AN: 151830 Hom.: 7736 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.301 AC: 45725 AN: 151948 Hom.: 7740 Cov.: 32 AF XY: 0.300 AC XY: 22265 AN XY: 74240

African (AFR) AF: 0.151 AC: 6280 AN: 41470

American (AMR) AF: 0.260 AC: 3977 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1640 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5166

South Asian (SAS) AF: 0.206 AC: 994 AN: 4816

European-Finnish (FIN) AF: 0.374 AC: 3927 AN: 10508

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25169 AN: 67936

Other (OTH) AF: 0.335 AC: 706 AN: 2108

Alfa AF: 0.320 Hom.: 1044

Bravo AF: 0.290

Asia WGS AF: 0.304 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2509851; hg19: chr11-118966780;