Variant chr1-20652339-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005216.5(DDOST):c.*40A>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 0.87 in 1,529,674 control chromosomes in the GnomAD database, including 579,708 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.84 ( 53971 hom., cov: 32)

Exomes 𝑓: 0.87 ( 525737 hom. )

Consequence

DDOST
NM_005216.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.10

Variant links:

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]

DDOST links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-20652339-T-C is Benign according to our data. Variant chr1-20652339-T-C is described in ClinVar as [Benign]. Clinvar id is 295057.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDOST	NM_005216.5 linkuse as main transcript	c.*40A>G		3_prime_UTR_variant	11/11	ENST00000602624.7	NP_005207.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDOST	ENST00000602624.7 linkuse as main transcript	c.*40A>G		3_prime_UTR_variant	11/11	1	NM_005216.5	ENSP00000473655	P1
DDOST	ENST00000415136.6 linkuse as main transcript	c.*40A>G		3_prime_UTR_variant	11/11	1		ENSP00000399457		P39656-1

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127779

AN:

152052

Hom.:

53937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.764

Gnomad AMI

AF:

0.837

Gnomad AMR

AF:

0.811

Gnomad ASJ

AF:

0.903

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.886

Gnomad FIN

AF:

0.904

Gnomad MID

AF:

0.902

Gnomad NFE

AF:

0.878

Gnomad OTH

AF:

0.866

GnomAD3 exomes

AF:

0.862

AC:

145250

AN:

168494

Hom.:

62788

AF XY:

0.867

AC XY:

78655

AN XY:

90736

show subpopulations

Gnomad AFR exome

AF:

0.769

Gnomad AMR exome

AF:

0.808

Gnomad ASJ exome

AF:

0.902

Gnomad EAS exome

AF:

0.822

Gnomad SAS exome

AF:

0.888

Gnomad FIN exome

AF:

0.910

Gnomad NFE exome

AF:

0.879

Gnomad OTH exome

AF:

0.875

GnomAD4 exome

AF:

0.873

AC:

1202625

AN:

1377504

Hom.:

525737

Cov.:

AF XY:

0.874

AC XY:

592512

AN XY:

678126

show subpopulations

Gnomad4 AFR exome

AF:

0.754

Gnomad4 AMR exome

AF:

0.806

Gnomad4 ASJ exome

AF:

0.901

Gnomad4 EAS exome

AF:

0.799

Gnomad4 SAS exome

AF:

0.885

Gnomad4 FIN exome

AF:

0.909

Gnomad4 NFE exome

AF:

0.878

Gnomad4 OTH exome

AF:

0.873

GnomAD4 genome

AF:

0.840

AC:

127870

AN:

152170

Hom.:

53971

Cov.:

AF XY:

0.842

AC XY:

62626

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.764

Gnomad4 AMR

AF:

0.811

Gnomad4 ASJ

AF:

0.903

Gnomad4 EAS

AF:

0.808

Gnomad4 SAS

AF:

0.886

Gnomad4 FIN

AF:

0.904

Gnomad4 NFE

AF:

0.879

Gnomad4 OTH

AF:

0.867

Alfa

AF:

0.865

Hom.:

16599

Bravo

AF:

0.830

Asia WGS

AF:

0.839

AC:

2916

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Congenital disorder of glycosylation type Ir

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 30, 2021

- -

Congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Parkinson Disease, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.6

DANN

Benign

0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over