13-70139383-A-ACTGCTGCTGCTG

Position:

• chr13-70139383-A-ACTGCTGCTGCTG

Variant summary

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

The NR_002717.2(ATXN8OS):​n.1137_1148dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0065 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0088 (313 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATXN8OS NR_002717.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 710 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.2	n.1137_1148dup		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000673087.1	n.48_49insCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000678624.1	n.500-7937_500-7926dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00651 AC: 710 AN: 109090 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.00140

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.00442

Gnomad FIN AF: 0.00384

Gnomad MID AF: 0.00781

Gnomad NFE AF: 0.00631

Gnomad OTH AF: 0.00710

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00879 AC: 3068 AN: 348980 Hom.: 313 Cov.: 0 AF XY: 0.00860 AC XY: 1600 AN XY: 186066

Gnomad4 AFR exome AF: 0.0159

Gnomad4 AMR exome AF: 0.00455

Gnomad4 ASJ exome AF: 0.00234

Gnomad4 EAS exome AF: 0.0126

Gnomad4 SAS exome AF: 0.00772

Gnomad4 FIN exome AF: 0.00405

Gnomad4 NFE exome AF: 0.00948

Gnomad4 OTH exome AF: 0.00829

GnomAD4 genome AF: 0.00651 AC: 710 AN: 109120 Hom.: 2 Cov.: 0 AF XY: 0.00661 AC XY: 348 AN XY: 52658

Gnomad4 AFR AF: 0.00928

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.00140

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.00443

Gnomad4 FIN AF: 0.00384

Gnomad4 NFE AF: 0.00631

Gnomad4 OTH AF: 0.00636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs193922930; hg19: chr13-70713515;