Variant chr13-70139377-ACTACTACTGCTGCTGCTG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

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

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

ATXN8OS (HGNC:10561): (ATXN8 opposite strand lncRNA) This gene is an antisense transcript to the KLHL1 gene (homolog to the Drosophila KELCH gene); it does not itself appear to be protein coding. A TAC/TGC trinucleotide repeat expansion that is incorporated into this gene transcript, but not the KLHL1 transcript, causes spinocerebellar ataxia type 8. Presumably the expansion interferes with normal antisense function of this transcript. [provided by RefSeq, Oct 2008]

ATXN8OS links:

ENSG00000288330 (HGNC:32925):

ENSG00000288330 links:

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ACMG classification

Classification made for transcript

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	Effect	Exon rank
ATXN8OS	NR_002717.3 link	n.891_908delACTACTGCTGCTGCTGCT	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	NR_185834.1 link	n.454-7975_454-7958delACTACTGCTGCTGCTGCT	intron_variant	Intron 3 of 4
ATXN8OS	NR_185835.1 link	n.454-7975_454-7958delACTACTGCTGCTGCTGCT	intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ATXN8OS	ENST00000414504.6 link	n.1099_1116delACTACTGCTGCTGCTGCT	non_coding_transcript_exon_variant	Exon 5 of 5	5
ENSG00000288330	ENST00000673087.1 link	n.37_54delCAGCAGCAGCAGTAGTAG	non_coding_transcript_exon_variant	Exon 1 of 1
ATXN8OS	ENST00000660386.1 link	n.451-7975_451-7958delACTACTGCTGCTGCTGCT	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0561

AC:

5505

AN:

98162

Hom.:

379

Cov.:

show subpopulations

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.:

AF XY:

0.00231

AC XY:

673

AN XY:

291336

show subpopulations

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.:

AF XY:

0.0557

AC XY:

2640

AN XY:

47380

show subpopulations

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.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ATXN8OS-related disorder

Benign:1

May 26, 2023

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over