chr13-70139377-ACTACTACTGCTGCTGCTG-A

Position:

• chr13-70139377-ACTACTACTGCTGCTGCTG-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NR_002717.3(ATXN8OS):​n.891_908delACTACTGCTGCTGCTGCT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 645,424 control chromosomes in the GnomAD database, including 415 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.056 (379 hom., cov: 0)
  • Exomes 𝑓: 0.0027 (36 hom.)
• Consequence: ATXN8OS NR_002717.3 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.50

Genes affected

ATXN8OS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 13-70139377-ACTACTACTGCTGCTGCTG-A is Benign according to our data. Variant chr13-70139377-ACTACTACTGCTGCTGCTG-A is described in ClinVar as [Benign]. Clinvar id is 3039106.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.891_908delACTACTGCTGCTGCTGCT		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7975_454-7958delACTACTGCTGCTGCTGCT		intron_variant
ATXN8OS	NR_185835.1	n.454-7975_454-7958delACTACTGCTGCTGCTGCT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN8OS	ENST00000414504.6	n.1099_1116delACTACTGCTGCTGCTGCT		non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1	n.37_54delCAGCAGCAGCAGTAGTAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7975_451-7958delACTACTGCTGCTGCTGCT		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 5505 AN: 98162 Hom.: 379 Cov.: 0

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0222

Gnomad ASJ AF: 0.00176

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00164

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0217

Gnomad NFE AF: 0.000997

Gnomad OTH AF: 0.0385

GnomAD4 exome AF: 0.00275 AC: 1504 AN: 547206 Hom.: 36 AF XY: 0.00231 AC XY: 673 AN XY: 291336

Gnomad4 AFR exome AF: 0.0763

Gnomad4 AMR exome AF: 0.00348

Gnomad4 ASJ exome AF: 0.0000554

Gnomad4 EAS exome AF: 0.0000335

Gnomad4 SAS exome AF: 0.0000203

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000396

Gnomad4 OTH exome AF: 0.00669

GnomAD4 genome AF: 0.0561 AC: 5510 AN: 98218 Hom.: 379 Cov.: 0 AF XY: 0.0557 AC XY: 2640 AN XY: 47380

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.00176

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00109

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000997

Gnomad4 OTH AF: 0.0385

Alfa AF: 0.0325 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

ATXN8OS-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 26, 2023

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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: rs1186729821; hg19: chr13-70713509;