rs142909469
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000113.3(TOR1A):c.488C>T(p.Ala163Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000113.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1A | NM_000113.3 | c.488C>T | p.Ala163Val | missense_variant | 3/5 | ENST00000351698.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1A | ENST00000351698.5 | c.488C>T | p.Ala163Val | missense_variant | 3/5 | 1 | NM_000113.3 | P1 | |
TOR1A | ENST00000651202.1 | c.584C>T | p.Ala195Val | missense_variant | 3/6 | ||||
TOR1A | ENST00000473604.2 | n.598C>T | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 76AN: 250954Hom.: 0 AF XY: 0.000332 AC XY: 45AN XY: 135682
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461524Hom.: 0 Cov.: 33 AF XY: 0.000311 AC XY: 226AN XY: 727080
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | TOR1A: BP4 - |
Dystonic disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Early-onset generalized limb-onset dystonia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Nov 01, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at