rs2509851

Positions:

• chr11-119096070-A-C
• chr11-119096070-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047426508.1(DPAGT1):​c.*928T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 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 XM_047426508.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DPAGT1	XM_047426508.1	c.*928T>G		3_prime_UTR_variant	9/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPAGT1	ENST00000682232.1	c.*1772T>G		3_prime_UTR_variant, NMD_transcript_variant	7/7

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.335

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2509851; hg19: chr11-118966780;