Variant rs35337578 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The ENST00000337523.10(DXO):c.744A>G(p.Pro248=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 1,612,802 control chromosomes in the GnomAD database, including 7,142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 869 hom., cov: 32)

Exomes 𝑓: 0.086 ( 6273 hom. )

Consequence

DXO
ENST00000337523.10 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.95

Variant links:

Genes affected

DXO (HGNC:2992): (decapping exoribonuclease) This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. The function of its protein product is unknown, but its ubiquitous expression and conservation in both simple and complex eukaryotes suggests that this may be a housekeeping gene. [provided by RefSeq, Jul 2008]

DXO links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 6-31970674-T-C is Benign according to our data. Variant chr6-31970674-T-C is described in ClinVar as [Benign]. Clinvar id is 403445.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.95 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DXO	NM_005510.4 linkuse as main transcript	c.744A>G	p.Pro248=	synonymous_variant	4/7	ENST00000337523.10	NP_005501.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DXO	ENST00000337523.10 linkuse as main transcript	c.744A>G	p.Pro248=	synonymous_variant	4/7	1	NM_005510.4	ENSP00000337759	P1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15404

AN:

151964

Hom.:

874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.0805

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.0366

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.0541

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0862

Gnomad OTH

AF:

0.121

GnomAD3 exomes

AF:

0.0898

AC:

22155

AN:

246806

Hom.:

1259

AF XY:

0.0916

AC XY:

12322

AN XY:

134448

show subpopulations

Gnomad AFR exome

AF:

0.150

Gnomad AMR exome

AF:

0.0750

Gnomad ASJ exome

AF:

0.180

Gnomad EAS exome

AF:

0.0338

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.0538

Gnomad NFE exome

AF:

0.0828

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0858

AC:

125283

AN:

1460720

Hom.:

6273

Cov.:

AF XY:

0.0869

AC XY:

63141

AN XY:

726676

show subpopulations

Gnomad4 AFR exome

AF:

0.152

Gnomad4 AMR exome

AF:

0.0784

Gnomad4 ASJ exome

AF:

0.178

Gnomad4 EAS exome

AF:

0.0213

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.0539

Gnomad4 NFE exome

AF:

0.0814

Gnomad4 OTH exome

AF:

0.0979

GnomAD4 genome

AF:

0.101

AC:

15407

AN:

152082

Hom.:

869

Cov.:

AF XY:

0.0997

AC XY:

7415

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0803

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.0368

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.0541

Gnomad4 NFE

AF:

0.0862

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.0938

Hom.:

483

Bravo

AF:

0.107

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

EpiCase

AF:

0.0980

EpiControl

AF:

0.0945

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.73

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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