13-70139383-A-ACTGCTGCTG

Position:

• chr13-70139383-A-ACTGCTGCTG

Variant summary

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

The NR_002717.3(ATXN8OS):​n.932_940dupTGCTGCTGC 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 0.0053 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0085 (251 hom.)
• Consequence: ATXN8OS NR_002717.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

ENSG00000288330 (HGNC:32925):

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 582 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.932_940dupTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7934_454-7926dupTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7934_454-7926dupTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288330	ENST00000673087.1	n.40_48dupCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7934_451-7926dupTGCTGCTGC		intron_variant
ATXN8OS	ENST00000677785.1	n.393-7934_393-7926dupTGCTGCTGC		intron_variant
ATXN8OS	ENST00000678624.1	n.500-7934_500-7926dupTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00534 AC: 582 AN: 109082 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00457

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00319

Gnomad ASJ AF: 0.00176

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.00691

Gnomad FIN AF: 0.00261

Gnomad MID AF: 0.0117

Gnomad NFE AF: 0.00607

Gnomad OTH AF: 0.00497

GnomAD4 exome AF: 0.00846 AC: 2952 AN: 348854 Hom.: 251 Cov.: 0 AF XY: 0.00847 AC XY: 1576 AN XY: 185994

Gnomad4 AFR exome AF: 0.0100

Gnomad4 AMR exome AF: 0.00804

Gnomad4 ASJ exome AF: 0.000918

Gnomad4 EAS exome AF: 0.00909

Gnomad4 SAS exome AF: 0.00962

Gnomad4 FIN exome AF: 0.00514

Gnomad4 NFE exome AF: 0.00904

Gnomad4 OTH exome AF: 0.00724

GnomAD4 genome AF: 0.00533 AC: 582 AN: 109112 Hom.: 3 Cov.: 0 AF XY: 0.00564 AC XY: 297 AN XY: 52640

Gnomad4 AFR AF: 0.00456

Gnomad4 AMR AF: 0.00319

Gnomad4 ASJ AF: 0.00176

Gnomad4 EAS AF: 0.0123

Gnomad4 SAS AF: 0.00693

Gnomad4 FIN AF: 0.00261

Gnomad4 NFE AF: 0.00609

Gnomad4 OTH AF: 0.00494

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;