13-70139383-ACTGCTGCTG-A

Position:

• chr13-70139383-ACTGCTGCTG-A

Variant summary

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

The ENST00000414504.6(ATXN8OS):​n.1140_1148delTGCTGCTGC variant causes a splice region, 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 0.0061 (3 hom., cov: 0)
  • Exomes 𝑓: 0.014 (334 hom.)
  • Failed GnomAD Quality Control
• 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 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.932_940delTGCTGCTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7934_454-7926delTGCTGCTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7934_454-7926delTGCTGCTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN8OS	ENST00000414504.6	n.1140_1148delTGCTGCTGC		splice_region_variant, non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1	n.40_48delCAGCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7934_451-7926delTGCTGCTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00610 AC: 665 AN: 109066 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00906

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.0422

Gnomad EAS AF: 0.00961

Gnomad SAS AF: 0.00608

Gnomad FIN AF: 0.000767

Gnomad MID AF: 0.0156

Gnomad NFE AF: 0.00395

Gnomad OTH AF: 0.00639

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0135 AC: 4567 AN: 338096 Hom.: 334 AF XY: 0.0145 AC XY: 2601 AN XY: 179838

Gnomad4 AFR exome AF: 0.00918

Gnomad4 AMR exome AF: 0.0240

Gnomad4 ASJ exome AF: 0.0407

Gnomad4 EAS exome AF: 0.00472

Gnomad4 SAS exome AF: 0.0313

Gnomad4 FIN exome AF: 0.00529

Gnomad4 NFE exome AF: 0.0109

Gnomad4 OTH exome AF: 0.0140

GnomAD4 genome AF: 0.00610 AC: 666 AN: 109096 Hom.: 3 Cov.: 0 AF XY: 0.00578 AC XY: 304 AN XY: 52640

Gnomad4 AFR AF: 0.00916

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.0422

Gnomad4 EAS AF: 0.00938

Gnomad4 SAS AF: 0.00609

Gnomad4 FIN AF: 0.000767

Gnomad4 NFE AF: 0.00395

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;