rs149514221
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000113.3(TOR1A):c.621-41A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000703 in 1,614,158 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 (★).
Frequency
Genomes: 𝑓 0.00040 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00073 ( 0 hom. )
Consequence
TOR1A
NM_000113.3 intron
NM_000113.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.62
Genes affected
TOR1A (HGNC:3098): (torsin family 1 member A) The protein encoded by this gene is a member of the AAA family of adenosine triphosphatases (ATPases), is related to the Clp protease/heat shock family and is expressed prominently in the substantia nigra pars compacta. Mutations in this gene result in the autosomal dominant disorder, torsion dystonia 1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 9-129818688-T-A is Benign according to our data. Variant chr9-129818688-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 255136.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1A | NM_000113.3 | c.621-41A>T | intron_variant | ENST00000351698.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1A | ENST00000351698.5 | c.621-41A>T | intron_variant | 1 | NM_000113.3 | P1 | |||
TOR1A | ENST00000651202.1 | c.717-41A>T | intron_variant | ||||||
TOR1A | ENST00000473604.2 | n.731-41A>T | intron_variant, non_coding_transcript_variant | 5 | |||||
TOR1A | ENST00000474192.1 | n.38-41A>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000407 AC: 62AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000382 AC: 96AN: 251348Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135868
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GnomAD4 exome AF: 0.000734 AC: 1073AN: 1461818Hom.: 0 Cov.: 32 AF XY: 0.000677 AC XY: 492AN XY: 727220
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GnomAD4 genome ? AF: 0.000400 AC: 61AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74492
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at