13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The NR_002717.3(ATXN8OS):​n.932_940dupTGCTGCTGC 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 0.0053 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0085 (251 hom.)
• 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 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.932_940dupTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7934_454-7926dupTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7934_454-7926dupTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288330	ENST00000673087.1	n.40_48dupCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7934_451-7926dupTGCTGCTGC		intron_variant
ATXN8OS	ENST00000677785.1	n.393-7934_393-7926dupTGCTGCTGC		intron_variant
ATXN8OS	ENST00000678624.1	n.500-7934_500-7926dupTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00534 AC: 582 AN: 109082 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00457

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00319

Gnomad ASJ AF: 0.00176

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.00691

Gnomad FIN AF: 0.00261

Gnomad MID AF: 0.0117

Gnomad NFE AF: 0.00607

Gnomad OTH AF: 0.00497

GnomAD4 exome AF: 0.00846 AC: 2952 AN: 348854 Hom.: 251 Cov.: 0 AF XY: 0.00847 AC XY: 1576 AN XY: 185994

Gnomad4 AFR exome AF: 0.0100

Gnomad4 AMR exome AF: 0.00804

Gnomad4 ASJ exome AF: 0.000918

Gnomad4 EAS exome AF: 0.00909

Gnomad4 SAS exome AF: 0.00962

Gnomad4 FIN exome AF: 0.00514

Gnomad4 NFE exome AF: 0.00904

Gnomad4 OTH exome AF: 0.00724

GnomAD4 genome AF: 0.00533 AC: 582 AN: 109112 Hom.: 3 Cov.: 0 AF XY: 0.00564 AC XY: 297 AN XY: 52640

Gnomad4 AFR AF: 0.00456

Gnomad4 AMR AF: 0.00319

Gnomad4 ASJ AF: 0.00176

Gnomad4 EAS AF: 0.0123

Gnomad4 SAS AF: 0.00693

Gnomad4 FIN AF: 0.00261

Gnomad4 NFE AF: 0.00609

Gnomad4 OTH AF: 0.00494

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;