13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The ENST00000414504.6(ATXN8OS):​n.1131_1148delTGCTGCTGCTGCTGCTGC 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 0.00848 in 457,394 control chromosomes in the GnomAD database, including 43 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.011 (17 hom., cov: 0)
  • Exomes 𝑓: 0.0077 (26 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.923_940delTGCTGCTGCTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7943_454-7926delTGCTGCTGCTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7943_454-7926delTGCTGCTGCTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN8OS	ENST00000414504.6	n.1131_1148delTGCTGCTGCTGCTGCTGC		splice_region_variant, non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1	n.31_48delCAGCAGCAGCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7943_451-7926delTGCTGCTGCTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0110 AC: 1205 AN: 109084 Hom.: 17 Cov.: 0

Gnomad AFR AF: 0.00461

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00411

Gnomad ASJ AF: 0.00702

Gnomad EAS AF: 0.00160

Gnomad SAS AF: 0.00442

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.00355

GnomAD4 exome AF: 0.00768 AC: 2675 AN: 348280 Hom.: 26 AF XY: 0.00737 AC XY: 1369 AN XY: 185630

Gnomad4 AFR exome AF: 0.00367

Gnomad4 AMR exome AF: 0.00134

Gnomad4 ASJ exome AF: 0.00284

Gnomad4 EAS exome AF: 0.00218

Gnomad4 SAS exome AF: 0.00119

Gnomad4 FIN exome AF: 0.0241

Gnomad4 NFE exome AF: 0.00857

Gnomad4 OTH exome AF: 0.00675

GnomAD4 genome AF: 0.0110 AC: 1204 AN: 109114 Hom.: 17 Cov.: 0 AF XY: 0.0120 AC XY: 634 AN XY: 52648

Gnomad4 AFR AF: 0.00456

Gnomad4 AMR AF: 0.00410

Gnomad4 ASJ AF: 0.00702

Gnomad4 EAS AF: 0.00161

Gnomad4 SAS AF: 0.00443

Gnomad4 FIN AF: 0.0383

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.00353

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;