13-70139383-A-ACTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-A-ACTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The NR_002717.2(ATXN8OS):​n.1128_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 0.00091 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00052 (7 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 99 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.2	n.1128_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_49insCAGCAGCAGCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000678624.1	n.500-7946_500-7926dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.000907 AC: 99 AN: 109110 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00100

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00160

Gnomad SAS AF: 0.000552

Gnomad FIN AF: 0.000153

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000165

Gnomad OTH AF: 0.000710

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000524 AC: 183 AN: 349186 Hom.: 7 Cov.: 0 AF XY: 0.000505 AC XY: 94 AN XY: 186194

Gnomad4 AFR exome AF: 0.00177

Gnomad4 AMR exome AF: 0.00118

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00323

Gnomad4 SAS exome AF: 0.000408

Gnomad4 FIN exome AF: 0.0000471

Gnomad4 NFE exome AF: 0.000157

Gnomad4 OTH exome AF: 0.00106

GnomAD4 genome AF: 0.000907 AC: 99 AN: 109140 Hom.: 1 Cov.: 0 AF XY: 0.000835 AC XY: 44 AN XY: 52666

Gnomad4 AFR AF: 0.00283

Gnomad4 AMR AF: 0.00100

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00161

Gnomad4 SAS AF: 0.000554

Gnomad4 FIN AF: 0.000153

Gnomad4 NFE AF: 0.000165

Gnomad4 OTH AF: 0.000706

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;