13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000414504.6(ATXN8OS):n.1119_1148delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 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 0.0000305 in 458,352 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000026 ( 0 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: 0.190
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN8OS | NR_002717.3 | n.911_940delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | non_coding_transcript_exon_variant | 5/5 | ||||
ATXN8OS | NR_185834.1 | n.454-7955_454-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant | |||||
ATXN8OS | NR_185835.1 | n.454-7955_454-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN8OS | ENST00000414504.6 | n.1119_1148delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | splice_region_variant, non_coding_transcript_exon_variant | 5/5 | 5 | |||||
ENSG00000288330 | ENST00000673087.1 | n.19_48delCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG | non_coding_transcript_exon_variant | 1/1 | ||||||
ATXN8OS | ENST00000660386.1 | n.451-7955_451-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0000458 AC: 5AN: 109116Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000258 AC: 9AN: 349206Hom.: 0 AF XY: 0.0000107 AC XY: 2AN XY: 186204
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GnomAD4 genome AF: 0.0000458 AC: 5AN: 109146Hom.: 0 Cov.: 0 AF XY: 0.0000380 AC XY: 2AN XY: 52666
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at