13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The NR_002717.3(ATXN8OS):​n.929_940dupTGCTGCTGCTGC 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 0.0065 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0088 (313 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.929_940dupTGCTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7937_454-7926dupTGCTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7937_454-7926dupTGCTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288330	ENST00000673087.1	n.37_48dupCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7937_451-7926dupTGCTGCTGCTGC		intron_variant
ATXN8OS	ENST00000677785.1	n.393-7937_393-7926dupTGCTGCTGCTGC		intron_variant
ATXN8OS	ENST00000678624.1	n.500-7937_500-7926dupTGCTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00651 AC: 710 AN: 109090 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.00140

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.00442

Gnomad FIN AF: 0.00384

Gnomad MID AF: 0.00781

Gnomad NFE AF: 0.00631

Gnomad OTH AF: 0.00710

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00879 AC: 3068 AN: 348980 Hom.: 313 Cov.: 0 AF XY: 0.00860 AC XY: 1600 AN XY: 186066

Gnomad4 AFR exome AF: 0.0159

Gnomad4 AMR exome AF: 0.00455

Gnomad4 ASJ exome AF: 0.00234

Gnomad4 EAS exome AF: 0.0126

Gnomad4 SAS exome AF: 0.00772

Gnomad4 FIN exome AF: 0.00405

Gnomad4 NFE exome AF: 0.00948

Gnomad4 OTH exome AF: 0.00829

GnomAD4 genome AF: 0.00651 AC: 710 AN: 109120 Hom.: 2 Cov.: 0 AF XY: 0.00661 AC XY: 348 AN XY: 52658

Gnomad4 AFR AF: 0.00928

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.00140

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.00443

Gnomad4 FIN AF: 0.00384

Gnomad4 NFE AF: 0.00631

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;