9-129813548-TA-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000113.3(TOR1A):c.*423del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 293,254 control chromosomes in the GnomAD database, including 50 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 18 hom., cov: 32)
Exomes 𝑓: 0.016 ( 32 hom. )
Consequence
TOR1A
NM_000113.3 3_prime_UTR
NM_000113.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.73
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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 9-129813548-TA-T is Benign according to our data. Variant chr9-129813548-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 365221.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0124 (1873/150984) while in subpopulation EAS AF= 0.0202 (104/5144). AF 95% confidence interval is 0.0171. There are 18 homozygotes in gnomad4. There are 899 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1A | NM_000113.3 | c.*423del | 3_prime_UTR_variant | 5/5 | ENST00000351698.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1A | ENST00000351698.5 | c.*423del | 3_prime_UTR_variant | 5/5 | 1 | NM_000113.3 | P1 | ||
TOR1A | ENST00000651202.1 | c.*690del | 3_prime_UTR_variant | 6/6 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1871AN: 150876Hom.: 18 Cov.: 32
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GnomAD4 exome AF: 0.0163 AC: 2321AN: 142270Hom.: 32 Cov.: 0 AF XY: 0.0165 AC XY: 1274AN XY: 77424
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GnomAD4 genome ? AF: 0.0124 AC: 1873AN: 150984Hom.: 18 Cov.: 32 AF XY: 0.0122 AC XY: 899AN XY: 73772
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early-onset generalized limb-onset dystonia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at