3-49510802-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004393.6(DAG1):āc.268A>Cā(p.Ser90Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000675 in 1,614,176 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S90G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004393.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAG1 | NM_004393.6 | c.268A>C | p.Ser90Arg | missense_variant | 2/3 | ENST00000308775.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAG1 | ENST00000308775.7 | c.268A>C | p.Ser90Arg | missense_variant | 2/3 | 1 | NM_004393.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250922Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135618
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461878Hom.: 2 Cov.: 74 AF XY: 0.0000990 AC XY: 72AN XY: 727236
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152298Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 18, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at