Genetic Variant ENSG00000288330:n.10_48dupCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG (chr13-70139383-A-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000673087.1(ENSG00000288330):n.10_48dupCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000064 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000052 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000288330
ENST00000673087.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

0 publications found

Variant links:

Genes affected

ENSG00000288330 (HGNC:32925):

ENSG00000288330 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 Gene-Disease associations (from GenCC):

spinocerebellar ataxia type 8
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ATXN8OS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
ATXN8OS	NR_002717.3 link	n.902_940dupTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	NR_185834.1 link	n.454-7964_454-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant	Intron 3 of 4
ATXN8OS	NR_185835.1 link	n.454-7964_454-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288330	ENST00000673087.1 link	n.10_48dupCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG	non_coding_transcript_exon_variant	Exon 1 of 1
ATXN8OS	ENST00000756272.1 link	n.775_813dupTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	ENST00000660386.1 link	n.451-7964_451-7926dupTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0000642

AC:

AN:

109116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000351

Gnomad EAS

AF:

0.000534

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000153

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000366

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000515

AC:

AN:

349204

Hom.:

Cov.:

AF XY:

0.0000430

AC XY:

AN XY:

186202

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

7908

American (AMR)

AF:

0.000160

AC:

AN:

18694

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11978

East Asian (EAS)

AF:

0.0000807

AC:

AN:

24792

South Asian (SAS)

AF:

0.00

AC:

AN:

26972

European-Finnish (FIN)

AF:

0.0000471

AC:

AN:

21224

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1578

European-Non Finnish (NFE)

AF:

0.0000463

AC:

AN:

216158

Other (OTH)

AF:

0.000101

AC:

AN:

19900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.406

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000642

AC:

AN:

109116

Hom.:

Cov.:

AF XY:

0.0000190

AC XY:

AN XY:

52594

show subpopulations

African (AFR)

AF:

0.0000411

AC:

AN:

24304

American (AMR)

AF:

0.00

AC:

AN:

10960

Ashkenazi Jewish (ASJ)

AF:

0.000351

AC:

AN:

2848

East Asian (EAS)

AF:

0.000534

AC:

AN:

3746

South Asian (SAS)

AF:

0.00

AC:

AN:

3620

European-Finnish (FIN)

AF:

0.000153

AC:

AN:

6518

Middle Eastern (MID)

AF:

0.00

AC:

AN:

256

European-Non Finnish (NFE)

AF:

0.0000366

AC:

AN:

54686

Other (OTH)

AF:

0.00

AC:

AN:

1408

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.432

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.4

Splicing

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

Publications

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13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over