rs148925426
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_004320.6(ATP2A1):c.159G>A(p.Val53Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000216 in 1,614,172 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004320.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 177AN: 152174Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000330 AC: 83AN: 251366Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135878
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461880Hom.: 2 Cov.: 32 AF XY: 0.000113 AC XY: 82AN XY: 727242
GnomAD4 genome AF: 0.00116 AC: 177AN: 152292Hom.: 2 Cov.: 32 AF XY: 0.00109 AC XY: 81AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Has not been previously published as pathogenic or benign to our knowledge; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. -
Brody myopathy Benign:1
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ATP2A1-related disorder Benign:1
This variant is classified as likely 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