13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000414504.6(ATXN8OS):​n.1137_1148delTGCTGCTGCTGC variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000585 in 458,136 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00093 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00048 (1 hom.)
• Consequence: ATXN8OS ENST00000414504.6 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

ATXN8OS (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.929_940delTGCTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7937_454-7926delTGCTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7937_454-7926delTGCTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN8OS	ENST00000414504.6	n.1137_1148delTGCTGCTGCTGC		splice_region_variant, non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1	n.37_48delCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7937_451-7926delTGCTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.000917 AC: 100 AN: 109110 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00350

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000182

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000153

Gnomad MID AF: 0.00391

Gnomad NFE AF: 0.000183

Gnomad OTH AF: 0.000710

GnomAD4 exome AF: 0.000476 AC: 166 AN: 348996 Hom.: 1 AF XY: 0.000398 AC XY: 74 AN XY: 186086

Gnomad4 AFR exome AF: 0.00533

Gnomad4 AMR exome AF: 0.00129

Gnomad4 ASJ exome AF: 0.00167

Gnomad4 EAS exome AF: 0.000444

Gnomad4 SAS exome AF: 0.000668

Gnomad4 FIN exome AF: 0.000141

Gnomad4 NFE exome AF: 0.000180

Gnomad4 OTH exome AF: 0.000453

GnomAD4 genome AF: 0.000935 AC: 102 AN: 109140 Hom.: 1 Cov.: 0 AF XY: 0.00114 AC XY: 60 AN XY: 52662

Gnomad4 AFR AF: 0.00357

Gnomad4 AMR AF: 0.000182

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000153

Gnomad4 NFE AF: 0.000183

Gnomad4 OTH AF: 0.000706

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;