ENST00000673087.1:n.34_48dupCAGCAGCAGCAGCAG

Variant names:

• chr13-70139383-A-ACTGCTGCTGCTGCTG
• rs193922930
• ENST00000673087.1:n.34_48dupCAGCAGCAGCAGCAG

Variant summary

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

The ENST00000673087.1(ENSG00000288330):​n.34_48dupCAGCAGCAGCAGCAG 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 0.0038 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0044 (228 hom.)
• Consequence: ENSG00000288330 ENST00000673087.1 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 412 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.926_940dupTGCTGCTGCTGCTGC		non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	NR_185834.1	n.454-7940_454-7926dupTGCTGCTGCTGCTGC		intron_variant	Intron 3 of 4
ATXN8OS	NR_185835.1	n.454-7940_454-7926dupTGCTGCTGCTGCTGC		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288330	ENST00000673087.1	n.34_48dupCAGCAGCAGCAGCAG		non_coding_transcript_exon_variant	Exon 1 of 1
ATXN8OS	ENST00000660386.1	n.451-7940_451-7926dupTGCTGCTGCTGCTGC		intron_variant	Intron 3 of 3
ATXN8OS	ENST00000677785.1	n.393-7940_393-7926dupTGCTGCTGCTGCTGC		intron_variant	Intron 3 of 7
ATXN8OS	ENST00000678624.1	n.500-7940_500-7926dupTGCTGCTGCTGCTGC		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.00378 AC: 412 AN: 109094 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00885

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00219

Gnomad ASJ AF: 0.00140

Gnomad EAS AF: 0.00988

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.00230

Gnomad MID AF: 0.0117

Gnomad NFE AF: 0.00192

Gnomad OTH AF: 0.00142

GnomAD4 exome AF: 0.00436 AC: 1522 AN: 349062 Hom.: 228 Cov.: 0 AF XY: 0.00426 AC XY: 792 AN XY: 186124

Gnomad4 AFR exome AF: 0.0125

Gnomad4 AMR exome AF: 0.00166

Gnomad4 ASJ exome AF: 0.00159

Gnomad4 EAS exome AF: 0.00779

Gnomad4 SAS exome AF: 0.00397

Gnomad4 FIN exome AF: 0.00179

Gnomad4 NFE exome AF: 0.00440

Gnomad4 OTH exome AF: 0.00407

GnomAD4 genome AF: 0.00378 AC: 412 AN: 109124 Hom.: 2 Cov.: 0 AF XY: 0.00363 AC XY: 191 AN XY: 52656

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.00219

Gnomad4 ASJ AF: 0.00140

Gnomad4 EAS AF: 0.00992

Gnomad4 SAS AF: 0.00194

Gnomad4 FIN AF: 0.00230

Gnomad4 NFE AF: 0.00192

Gnomad4 OTH AF: 0.00141

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;