rs145206990
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001382.4(DPAGT1):c.918-18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,613,696 control chromosomes in the GnomAD database, including 207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0083 ( 4 hom., cov: 32)
Exomes 𝑓: 0.014 ( 203 hom. )
Consequence
DPAGT1
NM_001382.4 intron
NM_001382.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0830
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 11-119097569-C-T is Benign according to our data. Variant chr11-119097569-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 258077.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00834 (1270/152272) while in subpopulation NFE AF= 0.0153 (1042/68024). AF 95% confidence interval is 0.0145. There are 4 homozygotes in gnomad4. There are 533 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPAGT1 | NM_001382.4 | c.918-18G>A | intron_variant | ENST00000354202.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPAGT1 | ENST00000354202.9 | c.918-18G>A | intron_variant | 1 | NM_001382.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00835 AC: 1270AN: 152154Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00787 AC: 1979AN: 251452Hom.: 21 AF XY: 0.00799 AC XY: 1086AN XY: 135910
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GnomAD4 exome AF: 0.0144 AC: 20987AN: 1461424Hom.: 203 Cov.: 33 AF XY: 0.0139 AC XY: 10124AN XY: 727046
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GnomAD4 genome ? AF: 0.00834 AC: 1270AN: 152272Hom.: 4 Cov.: 32 AF XY: 0.00716 AC XY: 533AN XY: 74454
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 19, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
DPAGT1-congenital disorder of glycosylation;C3553645:Congenital myasthenic syndrome 13 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 23, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | DPAGT1: BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at