3-49510558-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_004393.6(DAG1):c.24G>A(p.Ser8Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,512 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
DAG1
NM_004393.6 synonymous
NM_004393.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
Publications
0 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 2PInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Genomics England PanelApp, Orphanet
- muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- muscular dystrophy-dystroglycanopathy, type AInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- isolated asymptomatic elevation of creatine phosphokinaseInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 3-49510558-G-A is Benign according to our data. Variant chr3-49510558-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 539136.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
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.24G>A | p.Ser8Ser | synonymous | Exon 2 of 3 | NP_004384.5 | ||
| DAG1 | NM_001165928.4 | c.24G>A | p.Ser8Ser | synonymous | Exon 5 of 6 | NP_001159400.3 | |||
| DAG1 | NM_001177634.3 | c.24G>A | p.Ser8Ser | synonymous | Exon 5 of 6 | NP_001171105.2 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DAG1 | ENST00000308775.7 | TSL:1 MANE Select | c.24G>A | p.Ser8Ser | synonymous | Exon 2 of 3 | ENSP00000312435.2 | ||
| DAG1 | ENST00000479935.1 | TSL:1 | n.335G>A | non_coding_transcript_exon | Exon 1 of 2 | ||||
| DAG1 | ENST00000418588.6 | TSL:3 | c.24G>A | p.Ser8Ser | synonymous | Exon 3 of 4 | ENSP00000405859.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250524 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
250524
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461512Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 727052 show subpopulations
GnomAD4 exome
AF:
AC:
19
AN:
1461512
Hom.:
Cov.:
29
AF XY:
AC XY:
9
AN XY:
727052
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33470
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86250
European-Finnish (FIN)
AF:
AC:
0
AN:
53238
Middle Eastern (MID)
AF:
AC:
0
AN:
5622
European-Non Finnish (NFE)
AF:
AC:
17
AN:
1111992
Other (OTH)
AF:
AC:
1
AN:
60382
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9;C4511963:Autosomal recessive limb-girdle muscular dystrophy type 2P Benign:1
May 31, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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