chr1-20651917-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005216.5(DDOST):c.*462A>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 0.43 in 154,560 control chromosomes in the GnomAD database, including 14,503 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.43 ( 14285 hom., cov: 31)
Exomes 𝑓: 0.37 ( 218 hom. )
Consequence
DDOST
NM_005216.5 3_prime_UTR
NM_005216.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.12
Genes affected
DDOST (HGNC:2728): (dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit) This gene encodes a component of the oligosaccharyltransferase complex which catalyzes the transfer of high-mannose oligosaccharides to asparagine residues on nascent polypeptides in the lumen of the rough endoplasmic reticulum. The protein complex co-purifies with ribosomes. The product of this gene is also implicated in the processing of advanced glycation endproducts (AGEs), which form from non-enzymatic reactions between sugars and proteins or lipids and are associated with aging and hyperglycemia. [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=-0.93).
BP6
Variant 1-20651917-T-C is Benign according to our data. Variant chr1-20651917-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 295047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDOST | NM_005216.5 | c.*462A>G | 3_prime_UTR_variant | 11/11 | ENST00000602624.7 | NP_005207.3 | ||
PINK1-AS | NR_046507.1 | n.277A>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDOST | ENST00000602624.7 | c.*462A>G | 3_prime_UTR_variant | 11/11 | 1 | NM_005216.5 | ENSP00000473655 | P1 | ||
DDOST | ENST00000415136.6 | c.*462A>G | 3_prime_UTR_variant | 11/11 | 1 | ENSP00000399457 | ||||
PINK1-AS | ENST00000451424.1 | n.277A>G | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.431 AC: 65340AN: 151718Hom.: 14259 Cov.: 31
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GnomAD4 exome AF: 0.369 AC: 1006AN: 2724Hom.: 218 Cov.: 0 AF XY: 0.371 AC XY: 528AN XY: 1422
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GnomAD4 genome AF: 0.431 AC: 65421AN: 151836Hom.: 14285 Cov.: 31 AF XY: 0.431 AC XY: 32005AN XY: 74204
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Parkinson Disease, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at