rs757760067
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_015046.7(SETX):c.172C>T(p.His58Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015046.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151938Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461670Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727156
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151938Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74168
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The p.H58Y variant (also known as c.172C>T), located in coding exon 1 of the SETX gene, results from a C to T substitution at nucleotide position 172. The histidine at codon 58 is replaced by tyrosine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity. (http://gnomad.broadinstitute.org) Computational tools disagree on the variant's effect on normal protein function. -
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