chr19-41967724-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_152296.5(ATP1A3):c.2859C>T(p.Ala953=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,082 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. A953A) has been classified as Likely benign.
Frequency
Consequence
NM_152296.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.2859C>T | p.Ala953= | synonymous_variant | 21/23 | ENST00000648268.1 | |
ATP1A3 | NM_001256214.2 | c.2898C>T | p.Ala966= | synonymous_variant | 21/23 | ||
ATP1A3 | NM_001256213.2 | c.2892C>T | p.Ala964= | synonymous_variant | 21/23 | ||
ATP1A3 | XM_047438862.1 | c.2769C>T | p.Ala923= | synonymous_variant | 21/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.2859C>T | p.Ala953= | synonymous_variant | 21/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152082Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152082Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Submissions by phenotype
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at