rs1568661

Variant names:

• chr3-49483525-A-G
• rs1568661
• NM_004393.6:c.-117+13092A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-49483525-A-G
• chr3-49483525-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004393.6(DAG1):​c.-117+13092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,738 control chromosomes in the GnomAD database, including 16,606 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16606 hom., cov: 31)
• Consequence: DAG1 NM_004393.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 20 publications found

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 Gene-Disease associations (from GenCC):

• autosomal recessive limb-girdle muscular dystrophy type 2P

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Orphanet
• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• muscular dystrophy-dystroglycanopathy, type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• isolated asymptomatic elevation of creatine phosphokinase

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004393.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAG1	NM_004393.6	MANE Select	c.-117+13092A>G		intron	N/A	NP_004384.5
	DAG1	NM_001165928.4		c.-477-3729A>G		intron	N/A	NP_001159400.3
	DAG1	NM_001177634.3		c.-278-3729A>G		intron	N/A	NP_001171105.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAG1	ENST00000308775.7	TSL:1 MANE Select	c.-117+13092A>G		intron	N/A	ENSP00000312435.2
	DAG1	ENST00000418588.6	TSL:3	c.-117+6625A>G		intron	N/A	ENSP00000405859.2
	DAG1	ENST00000421560.6	TSL:4	c.-117+13251A>G		intron	N/A	ENSP00000412067.2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68335 AN: 151622 Hom.: 16593 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.443

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.451 AC: 68382 AN: 151738 Hom.: 16606 Cov.: 31 AF XY: 0.456 AC XY: 33799 AN XY: 74148

African (AFR) AF: 0.383 AC: 15846 AN: 41346

American (AMR) AF: 0.587 AC: 8930 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3462

East Asian (EAS) AF: 0.930 AC: 4810 AN: 5172

South Asian (SAS) AF: 0.688 AC: 3305 AN: 4804

European-Finnish (FIN) AF: 0.346 AC: 3651 AN: 10538

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29090 AN: 67896

Other (OTH) AF: 0.448 AC: 941 AN: 2100

Alfa AF: 0.434 Hom.: 5497

Bravo AF: 0.466

Asia WGS AF: 0.779 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1568661; hg19: chr3-49520958;