3-49530895-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_004393.6(DAG1):c.384G>T(p.Val128Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000537 in 1,614,146 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004393.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DAG1 | NM_004393.6 | c.384G>T | p.Val128Val | synonymous_variant | Exon 3 of 3 | ENST00000308775.7 | NP_004384.5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00294 AC: 447AN: 152172Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000824 AC: 207AN: 251240Hom.: 4 AF XY: 0.000574 AC XY: 78AN XY: 135802
GnomAD4 exome AF: 0.000288 AC: 421AN: 1461856Hom.: 1 Cov.: 32 AF XY: 0.000245 AC XY: 178AN XY: 727226
GnomAD4 genome AF: 0.00293 AC: 446AN: 152290Hom.: 4 Cov.: 32 AF XY: 0.00278 AC XY: 207AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1
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
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DAG1-related disorder Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at