rs3814834
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000503767.5(ATXN3):c.-31C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,607,266 control chromosomes in the GnomAD database, including 12,782 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 0.17 ( 3181 hom., cov: 30)
Exomes 𝑓: 0.11 ( 9601 hom. )
Consequence
ATXN3
ENST00000503767.5 5_prime_UTR
ENST00000503767.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.180
Genes affected
ATXN3 (HGNC:7106): (ataxin 3) Machado-Joseph disease, also known as spinocerebellar ataxia-3, is an autosomal dominant neurologic disorder. The protein encoded by this gene contains (CAG)n repeats in the coding region, and the expansion of these repeats from the normal 12-44 to 52-86 is one cause of Machado-Joseph disease. There is a negative correlation between the age of onset and CAG repeat numbers. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2016]
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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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN3 | NM_004993.6 | upstream_gene_variant | ENST00000644486.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN3 | ENST00000644486.2 | upstream_gene_variant | NM_004993.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.169 AC: 25349AN: 150408Hom.: 3171 Cov.: 30
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GnomAD3 exomes AF: 0.111 AC: 26567AN: 239344Hom.: 2165 AF XY: 0.109 AC XY: 14194AN XY: 130804
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GnomAD4 exome AF: 0.105 AC: 153076AN: 1456756Hom.: 9601 Cov.: 32 AF XY: 0.105 AC XY: 76029AN XY: 724690
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GnomAD4 genome ? AF: 0.169 AC: 25385AN: 150510Hom.: 3181 Cov.: 30 AF XY: 0.166 AC XY: 12214AN XY: 73580
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at