chr13-70139383-ACTGCTGCTG-A

Position:

• chr13-70139383-ACTGCTGCTG-A

Variant summary

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

The NR_002717.2(ATXN8OS):​n.1140_1148del 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 0.0061 (3 hom., cov: 0)
  • Exomes 𝑓: 0.014 (334 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATXN8OS NR_002717.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

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 666 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.2	n.1140_1148del		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000673087.1	n.40_48del		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000678624.1	n.500-7934_500-7926del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00610 AC: 665 AN: 109066 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00906

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.0422

Gnomad EAS AF: 0.00961

Gnomad SAS AF: 0.00608

Gnomad FIN AF: 0.000767

Gnomad MID AF: 0.0156

Gnomad NFE AF: 0.00395

Gnomad OTH AF: 0.00639

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0135 AC: 4567 AN: 338096 Hom.: 334 AF XY: 0.0145 AC XY: 2601 AN XY: 179838

Gnomad4 AFR exome AF: 0.00918

Gnomad4 AMR exome AF: 0.0240

Gnomad4 ASJ exome AF: 0.0407

Gnomad4 EAS exome AF: 0.00472

Gnomad4 SAS exome AF: 0.0313

Gnomad4 FIN exome AF: 0.00529

Gnomad4 NFE exome AF: 0.0109

Gnomad4 OTH exome AF: 0.0140

GnomAD4 genome AF: 0.00610 AC: 666 AN: 109096 Hom.: 3 Cov.: 0 AF XY: 0.00578 AC XY: 304 AN XY: 52640

Gnomad4 AFR AF: 0.00916

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.0422

Gnomad4 EAS AF: 0.00938

Gnomad4 SAS AF: 0.00609

Gnomad4 FIN AF: 0.000767

Gnomad4 NFE AF: 0.00395

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;