chr13-70139383-ACTGCTGCTGCTGCTGCTG-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The ENST00000414504.6(ATXN8OS):n.1131_1148delTGCTGCTGCTGCTGCTGC 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 0.00848 in 457,394 control chromosomes in the GnomAD database, including 43 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.011 ( 17 hom., cov: 0)
Exomes 𝑓: 0.0077 ( 26 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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 1204 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN8OS | NR_002717.3 | n.923_940delTGCTGCTGCTGCTGCTGC | non_coding_transcript_exon_variant | 5/5 | ||||
ATXN8OS | NR_185834.1 | n.454-7943_454-7926delTGCTGCTGCTGCTGCTGC | intron_variant | |||||
ATXN8OS | NR_185835.1 | n.454-7943_454-7926delTGCTGCTGCTGCTGCTGC | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN8OS | ENST00000414504.6 | n.1131_1148delTGCTGCTGCTGCTGCTGC | splice_region_variant, non_coding_transcript_exon_variant | 5/5 | 5 | |||||
ENSG00000288330 | ENST00000673087.1 | n.31_48delCAGCAGCAGCAGCAGCAG | non_coding_transcript_exon_variant | 1/1 | ||||||
ATXN8OS | ENST00000660386.1 | n.451-7943_451-7926delTGCTGCTGCTGCTGCTGC | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1205AN: 109084Hom.: 17 Cov.: 0
GnomAD3 genomes
AF:
AC:
1205
AN:
109084
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00768 AC: 2675AN: 348280Hom.: 26 AF XY: 0.00737 AC XY: 1369AN XY: 185630
GnomAD4 exome
AF:
AC:
2675
AN:
348280
Hom.:
AF XY:
AC XY:
1369
AN XY:
185630
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0110 AC: 1204AN: 109114Hom.: 17 Cov.: 0 AF XY: 0.0120 AC XY: 634AN XY: 52648
GnomAD4 genome
AF:
AC:
1204
AN:
109114
Hom.:
Cov.:
0
AF XY:
AC XY:
634
AN XY:
52648
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at