Variant 13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000414504.6(ATXN8OS):n.1122_1148delTGCTGCTGCTGCTGCTGCTGCTGCTGC 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 0.000118 in 458,318 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 0.000082 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

ATXN8OS
ENST00000414504.6 splice_region, non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

Variant links:

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]

ATXN8OS links:

ENSG00000288330 (HGNC:32925):

ENSG00000288330 links:

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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 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
ATXN8OS	NR_002717.3 link	n.914_940delTGCTGCTGCTGCTGCTGCTGCTGCTGC	non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1 link	n.454-7952_454-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant
ATXN8OS	NR_185835.1 link	n.454-7952_454-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ATXN8OS	ENST00000414504.6 link	n.1122_1148delTGCTGCTGCTGCTGCTGCTGCTGCTGC	splice_region_variant, non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1 link	n.22_48delCAGCAGCAGCAGCAGCAGCAGCAGCAG	non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1 link	n.451-7952_451-7926delTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0000825

AC:

AN:

109116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000146

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000129

AC:

AN:

349202

Hom.:

AF XY:

0.000124

AC XY:

AN XY:

186198

show subpopulations

Gnomad4 AFR exome

AF:

0.000126

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000190

Gnomad4 OTH exome

AF:

0.000151

GnomAD4 genome

AF:

0.0000825

AC:

AN:

109116

Hom.:

Cov.:

AF XY:

0.0000570

AC XY:

AN XY:

52594

show subpopulations

Gnomad4 AFR

AF:

0.0000411

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000146

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over