rs2296793
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000113.3(TOR1A):c.246C>T(p.Ala82Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,613,904 control chromosomes in the GnomAD database, including 45,524 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000113.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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TOR1A | ENST00000351698.5 | c.246C>T | p.Ala82Ala | synonymous_variant | Exon 2 of 5 | 1 | NM_000113.3 | ENSP00000345719.4 | ||
TOR1A | ENST00000473084.1 | n.265C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
TOR1A | ENST00000651202.1 | c.342C>T | p.Ala114Ala | synonymous_variant | Exon 2 of 6 | ENSP00000498222.1 | ||||
TOR1A | ENST00000473604.2 | n.356C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.229 AC: 34865AN: 151944Hom.: 4076 Cov.: 32
GnomAD3 exomes AF: 0.224 AC: 56225AN: 251480Hom.: 6381 AF XY: 0.226 AC XY: 30775AN XY: 135916
GnomAD4 exome AF: 0.237 AC: 346107AN: 1461840Hom.: 41449 Cov.: 34 AF XY: 0.236 AC XY: 171551AN XY: 727218
GnomAD4 genome AF: 0.229 AC: 34877AN: 152064Hom.: 4075 Cov.: 32 AF XY: 0.229 AC XY: 17033AN XY: 74324
ClinVar
Submissions by phenotype
not specified Benign:4
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This variant is classified as Benign based on local population frequency. This variant was detected in 40% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 37. Only high quality variants are reported. -
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not provided Benign:2
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Dystonic disorder Benign:1
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Early-onset generalized limb-onset dystonia Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at