rs782459932
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_152296.5(ATP1A3):c.753G>A(p.Thr251=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,096 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T251T) has been classified as Likely benign.
Frequency
Consequence
NM_152296.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.753G>A | p.Thr251= | synonymous_variant | 8/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.792G>A | p.Thr264= | synonymous_variant | 8/23 | ||
ATP1A3 | NM_001256213.2 | c.786G>A | p.Thr262= | synonymous_variant | 8/23 | ||
ATP1A3 | XM_047438862.1 | c.663G>A | p.Thr221= | synonymous_variant | 8/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.753G>A | p.Thr251= | synonymous_variant | 8/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248376Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134478
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460936Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726646
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74336
ClinVar
Submissions by phenotype
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 11, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at