13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The NR_002717.3(ATXN8OS):​n.914_940dupTGCTGCTGCTGCTGCTGCTGCTGCTGC 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 0.00064 (2 hom., cov: 0)
  • Exomes 𝑓: 0.00030 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATXN8OS NR_002717.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

ENSG00000288330 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.914_940dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7952_454-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7952_454-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288330	ENST00000673087.1	n.22_48dupCAGCAGCAGCAGCAGCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7952_451-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		intron_variant
ATXN8OS	ENST00000677785.1	n.393-7952_393-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		intron_variant
ATXN8OS	ENST00000678624.1	n.500-7952_500-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.000642 AC: 70 AN: 109108 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000617

Gnomad AMI AF: 0.0470

Gnomad AMR AF: 0.000274

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00133

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000153

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000183

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000298 AC: 104 AN: 349190 Hom.: 3 Cov.: 0 AF XY: 0.000301 AC XY: 56 AN XY: 186194

Gnomad4 AFR exome AF: 0.000632

Gnomad4 AMR exome AF: 0.000214

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00141

Gnomad4 SAS exome AF: 0.000371

Gnomad4 FIN exome AF: 0.000236

Gnomad4 NFE exome AF: 0.000180

Gnomad4 OTH exome AF: 0.000302

GnomAD4 genome AF: 0.000641 AC: 70 AN: 109138 Hom.: 2 Cov.: 0 AF XY: 0.000646 AC XY: 34 AN XY: 52662

Gnomad4 AFR AF: 0.000616

Gnomad4 AMR AF: 0.000273

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00134

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000153

Gnomad4 NFE AF: 0.000183

Gnomad4 OTH AF: 0.00

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;