Variant chr13-70139383-A-ACTGCTG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NR_002717.2(ATXN8OS):n.1143_1148dup 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 0.015 ( 16 hom., cov: 0)

Exomes 𝑓: 0.015 ( 327 hom. )

Consequence

ATXN8OS
NR_002717.2 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Variant links:

Genes affected

(HGNC:):

links:

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0147 (1607/109100) while in subpopulation EAS AF= 0.0257 (96/3730). AF 95% confidence interval is 0.0216. There are 16 homozygotes in gnomad4. There are 788 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1607 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.2 linkuse as main transcript	n.1143_1148dup		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000673087.1 linkuse as main transcript	n.48_49insCAGCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000678624.1 linkuse as main transcript	n.500-7931_500-7926dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0147

AC:

1606

AN:

109070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0163

Gnomad AMI

AF:

0.0597

Gnomad AMR

AF:

0.0225

Gnomad ASJ

AF:

0.0379

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.00884

Gnomad FIN

AF:

0.00506

Gnomad MID

AF:

0.0508

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.0185

GnomAD4 exome

AF:

0.0154

AC:

5359

AN:

348650

Hom.:

327

Cov.:

AF XY:

0.0150

AC XY:

2779

AN XY:

185878

show subpopulations

Gnomad4 AFR exome

AF:

0.0194

Gnomad4 AMR exome

AF:

0.0138

Gnomad4 ASJ exome

AF:

0.0361

Gnomad4 EAS exome

AF:

0.0115

Gnomad4 SAS exome

AF:

0.0104

Gnomad4 FIN exome

AF:

0.00896

Gnomad4 NFE exome

AF:

0.0157

Gnomad4 OTH exome

AF:

0.0174

GnomAD4 genome

AF:

0.0147

AC:

1607

AN:

109100

Hom.:

Cov.:

AF XY:

0.0150

AC XY:

788

AN XY:

52638

show subpopulations

Gnomad4 AFR

AF:

0.0162

Gnomad4 AMR

AF:

0.0224

Gnomad4 ASJ

AF:

0.0379

Gnomad4 EAS

AF:

0.0257

Gnomad4 SAS

AF:

0.00886

Gnomad4 FIN

AF:

0.00506

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.0191

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over