Variant 1-20651922-T-G 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.*457A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 155,672 control chromosomes in the GnomAD database, including 314 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.053 ( 309 hom., cov: 31)

Exomes 𝑓: 0.059 ( 5 hom. )

Consequence

DDOST
NM_005216.5 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.398

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:

PINK1-AS (HGNC:38872): (PINK1 antisense RNA)

PINK1-AS 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=-0.87).

BP6

Variant 1-20651922-T-G is Benign according to our data. Variant chr1-20651922-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 295048.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0759 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.*457A>C		3_prime_UTR_variant	11/11	ENST00000602624.7	NP_005207.3
PINK1-AS	NR_046507.1 linkuse as main transcript	n.272A>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDOST	ENST00000602624.7 linkuse as main transcript	c.*457A>C	3_prime_UTR_variant	11/11	1	NM_005216.5	ENSP00000473655	P1
DDOST	ENST00000415136.6 linkuse as main transcript	c.*457A>C	3_prime_UTR_variant	11/11	1		ENSP00000399457		P39656-1
PINK1-AS	ENST00000451424.1 linkuse as main transcript	n.272A>C	non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.0534

AC:

8115

AN:

152010

Hom.:

309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0131

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0437

Gnomad ASJ

AF:

0.0366

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0460

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0777

Gnomad OTH

AF:

0.0505

GnomAD4 exome

AF:

0.0593

AC:

210

AN:

3544

Hom.:

Cov.:

AF XY:

0.0590

AC XY:

111

AN XY:

1880

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0249

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0317

Gnomad4 FIN exome

AF:

0.0682

Gnomad4 NFE exome

AF:

0.0721

Gnomad4 OTH exome

AF:

0.0662

GnomAD4 genome

AF:

0.0533

AC:

8110

AN:

152128

Hom.:

309

Cov.:

AF XY:

0.0534

AC XY:

3969

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0131

Gnomad4 AMR

AF:

0.0435

Gnomad4 ASJ

AF:

0.0366

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0465

Gnomad4 FIN

AF:

0.100

Gnomad4 NFE

AF:

0.0776

Gnomad4 OTH

AF:

0.0500

Alfa

AF:

0.0647

Hom.:

Bravo

AF:

0.0472

Asia WGS

AF:

0.0200

AC:

AN:

3478

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.9

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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