rs3737813
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001199260.2(TOR1AIP2):c.-147+4559T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 985,348 control chromosomes in the GnomAD database, including 14,678 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1796 hom., cov: 32)
Exomes 𝑓: 0.17 ( 12882 hom. )
Consequence
TOR1AIP2
NM_001199260.2 intron
NM_001199260.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0610
Genes affected
TOR1AIP2 (HGNC:24055): (torsin 1A interacting protein 2) One of the two protein isoforms encoded by this gene is a type II integral membrane protein found in the endoplasmic reticulum (ER). The encoded protein is a cofactor for the ATPase TorsinA, regulating the amount of TorsinA present in the ER compared to that found in the nuclear envelope. Defects in this protein are a cause of early onset primary dystonia, a neuromuscular disease. The other isoform encoded by this gene is an interferon alpha responsive protein whose cellular role has yet to be determined. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1AIP2 | NM_001199260.2 | c.-147+4559T>G | intron_variant | ENST00000609928.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1AIP2 | ENST00000609928.6 | c.-147+4559T>G | intron_variant | 2 | NM_001199260.2 | P1 | |||
TOR1AIP2 | ENST00000367612.7 | c.-146-8066T>G | intron_variant | 1 | P1 | ||||
TOR1AIP2 | ENST00000482587.5 | c.*3904T>G | 3_prime_UTR_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21256AN: 152122Hom.: 1794 Cov.: 32
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GnomAD4 exome AF: 0.174 AC: 144866AN: 833108Hom.: 12882 Cov.: 32 AF XY: 0.175 AC XY: 67196AN XY: 384714
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GnomAD4 genome ? AF: 0.140 AC: 21252AN: 152240Hom.: 1796 Cov.: 32 AF XY: 0.144 AC XY: 10704AN XY: 74440
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at