rs141696210
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_152296.5(ATP1A3):c.531C>T(p.Val177=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,614,098 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. V177V) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.531C>T | p.Val177= | synonymous_variant | 6/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.570C>T | p.Val190= | synonymous_variant | 6/23 | ||
ATP1A3 | NM_001256213.2 | c.564C>T | p.Val188= | synonymous_variant | 6/23 | ||
ATP1A3 | XM_047438862.1 | c.441C>T | p.Val147= | synonymous_variant | 6/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.531C>T | p.Val177= | synonymous_variant | 6/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251474Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135912
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727244
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74420
ClinVar
Submissions by phenotype
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at