9-132297025-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015046.7(SETX):āc.5811T>Cā(p.Asp1937Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,612,012 control chromosomes in the GnomAD database, including 51,483 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_015046.7 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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SETX | ENST00000224140.6 | c.5811T>C | p.Asp1937Asp | synonymous_variant | Exon 14 of 26 | 1 | NM_015046.7 | ENSP00000224140.5 | ||
SETX | ENST00000436441.5 | c.537T>C | p.Asp179Asp | synonymous_variant | Exon 4 of 17 | 5 | ENSP00000409143.1 |
Frequencies
GnomAD3 genomes AF: 0.317 AC: 48155AN: 151882Hom.: 10981 Cov.: 32
GnomAD3 exomes AF: 0.265 AC: 66348AN: 249954Hom.: 12526 AF XY: 0.260 AC XY: 35190AN XY: 135194
GnomAD4 exome AF: 0.199 AC: 290173AN: 1460014Hom.: 40460 Cov.: 32 AF XY: 0.202 AC XY: 147009AN XY: 726382
GnomAD4 genome AF: 0.317 AC: 48251AN: 151998Hom.: 11023 Cov.: 32 AF XY: 0.320 AC XY: 23733AN XY: 74266
ClinVar
Submissions by phenotype
not specified Benign:10
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -
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not provided Benign:3
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Amyotrophic lateral sclerosis type 4 Benign:2
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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. -
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 Benign:2
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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. -
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2;C1865409:Amyotrophic lateral sclerosis type 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at