rs627897
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015602.4(TOR1AIP1):c.1503G>A(p.Ala501=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 1,614,166 control chromosomes in the GnomAD database, including 728,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.93 ( 66292 hom., cov: 33)
Exomes 𝑓: 0.95 ( 662548 hom. )
Consequence
TOR1AIP1
NM_015602.4 synonymous
NM_015602.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0140
Genes affected
TOR1AIP1 (HGNC:29456): (torsin 1A interacting protein 1) This gene encodes a type 2 integral membrane protein that binds A- and B-type lamins. The encoded protein localizes to the inner nuclear membrane and may be involved in maintaining the attachment of the nuclear membrane to the nuclear lamina during cell division. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 1-179917990-G-A is Benign according to our data. Variant chr1-179917990-G-A is described in ClinVar as [Benign]. Clinvar id is 257698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-179917990-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.014 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1AIP1 | NM_015602.4 | c.1503G>A | p.Ala501= | synonymous_variant | 10/10 | ENST00000606911.7 | |
TOR1AIP1 | NM_001267578.2 | c.1506G>A | p.Ala502= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1AIP1 | ENST00000606911.7 | c.1503G>A | p.Ala501= | synonymous_variant | 10/10 | 1 | NM_015602.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.932 AC: 141871AN: 152154Hom.: 66244 Cov.: 33
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GnomAD3 exomes AF: 0.950 AC: 238682AN: 251342Hom.: 113448 AF XY: 0.951 AC XY: 129221AN XY: 135840
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GnomAD4 exome AF: 0.952 AC: 1391452AN: 1461894Hom.: 662548 Cov.: 82 AF XY: 0.952 AC XY: 692399AN XY: 727248
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GnomAD4 genome ? AF: 0.932 AC: 141977AN: 152272Hom.: 66292 Cov.: 33 AF XY: 0.933 AC XY: 69488AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2Y Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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