3-49510793-A-G

Position:

chr3-49510793-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004393.6(DAG1):c.259A>G(p.Ile87Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,614,076 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. I87I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0079 ( 7 hom., cov: 31)

Exomes 𝑓: 0.011 ( 106 hom. )

Consequence

DAG1
NM_004393.6 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6O:1

Conservation

PhyloP100: 2.26

Variant links:

Genes affected

DAG1 (HGNC:2666): (dystroglycan 1) This gene encodes dystroglycan, a central component of dystrophin-glycoprotein complex that links the extracellular matrix and the cytoskeleton in the skeletal muscle. The encoded preproprotein undergoes O- and N-glycosylation, and proteolytic processing to generate alpha and beta subunits. Certain mutations in this gene are known to cause distinct forms of muscular dystrophy. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Nov 2015]

DAG1 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 (MetaRNN=0.012165487).

BP6

Variant 3-49510793-A-G is Benign according to our data. Variant chr3-49510793-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 128884.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-49510793-A-G is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00791 (1204/152204) while in subpopulation AMR AF= 0.0193 (295/15280). AF 95% confidence interval is 0.0175. There are 7 homozygotes in gnomad4. There are 526 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAG1	NM_004393.6 linkuse as main transcript	c.259A>G	p.Ile87Val	missense_variant	2/3	ENST00000308775.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAG1	ENST00000308775.7 linkuse as main transcript	c.259A>G	p.Ile87Val	missense_variant	2/3	1	NM_004393.6	P1

Frequencies

GnomAD3 genomes

AF:

0.00791

AC:

1203

AN:

152086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00453

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.00809

AC:

2032

AN:

251050

Hom.:

AF XY:

0.00761

AC XY:

1033

AN XY:

135668

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.0159

Gnomad ASJ exome

AF:

0.00417

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00610

Gnomad NFE exome

AF:

0.0107

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.0107

AC:

15642

AN:

1461872

Hom.:

106

Cov.:

AF XY:

0.0102

AC XY:

7433

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.0164

Gnomad4 ASJ exome

AF:

0.00398

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.00640

Gnomad4 NFE exome

AF:

0.0124

Gnomad4 OTH exome

AF:

0.00942

GnomAD4 genome

AF:

0.00791

AC:

1204

AN:

152204

Hom.:

Cov.:

AF XY:

0.00707

AC XY:

526

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.0193

Gnomad4 ASJ

AF:

0.00375

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00453

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00974

Hom.:

Bravo

AF:

0.00922

TwinsUK

AF:

0.0127

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.0116

AC:

100

ExAC

AF:

0.00719

AC:

873

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0111

EpiControl

AF:

0.0113

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2Other:1

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 06, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Sep 12, 2017	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpretted as Likely benign and reported on 09-19-2018 by Lab or GTR ID 239772. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

not specified

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 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. -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9;C4511963:Autosomal recessive limb-girdle muscular dystrophy type 2P

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

DAG1-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 27, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Uncertain

-0.080

CADD

Benign

DANN

Benign

0.87

DEOGEN2

Benign

0.32

T;T;T;T;T;T;T;.;.;T

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.10

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.69

T;T;.;.;.;.;.;T;T;T

MetaRNN

Benign

0.012

T;T;T;T;T;T;T;T;T;T

MetaSVM

Uncertain

0.096

MutationAssessor

Benign

1.6

L;.;L;L;L;L;L;.;.;.

MutationTaster

Benign

0.93

N;N;N;N;N;N

PrimateAI

Benign

0.47

PROVEAN

Benign

-0.14

N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.23

Sift

Benign

0.25

T;D;T;T;T;T;T;D;T;D

Sift4G

Benign

0.54

T;D;T;T;T;T;T;D;D;D

Polyphen

0.0060

B;.;B;B;B;B;B;.;.;.

Vest4

0.17

MVP

0.72

MPC

0.23

ClinPred

0.0052

GERP RS

4.3

Varity_R

0.043

gMVP

0.35

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