13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000414504.6(ATXN8OS):n.1146_1148delTGC variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 454,152 control chromosomes in the GnomAD database, including 199 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.025 ( 33 hom., cov: 0)
Exomes 𝑓: 0.024 ( 166 hom. )
Consequence
ATXN8OS
ENST00000414504.6 splice_region, non_coding_transcript_exon
ENST00000414504.6 splice_region, non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.420
Genes affected
ATXN8OS (HGNC:10561): (ATXN8 opposite strand lncRNA) This gene is an antisense transcript to the KLHL1 gene (homolog to the Drosophila KELCH gene); it does not itself appear to be protein coding. A TAC/TGC trinucleotide repeat expansion that is incorporated into this gene transcript, but not the KLHL1 transcript, causes spinocerebellar ataxia type 8. Presumably the expansion interferes with normal antisense function of this transcript. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN8OS | ENST00000414504.6 | n.1146_1148delTGC | splice_region_variant, non_coding_transcript_exon_variant | 5/5 | 5 | |||||
ENSG00000288330 | ENST00000673087.1 | n.46_48delCAG | non_coding_transcript_exon_variant | 1/1 | ||||||
ATXN8OS | ENST00000660386.1 | n.451-7928_451-7926delTGC | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0250 AC: 2729AN: 108972Hom.: 33 Cov.: 0
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GnomAD4 exome AF: 0.0235 AC: 8119AN: 345150Hom.: 166 AF XY: 0.0243 AC XY: 4461AN XY: 183850
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GnomAD4 genome AF: 0.0251 AC: 2731AN: 109002Hom.: 33 Cov.: 0 AF XY: 0.0250 AC XY: 1313AN XY: 52588
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at