Genetic Variant ENSG00000288330:n.40_48dupCAGCAGCAG (chr13-70139383-A-ACTGCTGCTG) – 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.40_48dupCAGCAGCAG 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 0.0053 ( 3 hom., cov: 0)

Exomes 𝑓: 0.0085 ( 251 hom. )

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 582 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
ATXN8OS	NR_002717.3 link	n.932_940dupTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	NR_185834.1 link	n.454-7934_454-7926dupTGCTGCTGC	intron_variant	Intron 3 of 4
ATXN8OS	NR_185835.1 link	n.454-7934_454-7926dupTGCTGCTGC	intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288330	ENST00000673087.1 link	n.40_48dupCAGCAGCAG	non_coding_transcript_exon_variant	Exon 1 of 1
ATXN8OS	ENST00000756272.1 link	n.805_813dupTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	ENST00000660386.1 link	n.451-7934_451-7926dupTGCTGCTGC	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.00534

AC:

582

AN:

109082

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00457

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00319

Gnomad ASJ

AF:

0.00176

Gnomad EAS

AF:

0.0126

Gnomad SAS

AF:

0.00691

Gnomad FIN

AF:

0.00261

Gnomad MID

AF:

0.0117

Gnomad NFE

AF:

0.00607

Gnomad OTH

AF:

0.00497

GnomAD4 exome

AF:

0.00846

AC:

2952

AN:

348854

Hom.:

251

Cov.:

AF XY:

0.00847

AC XY:

1576

AN XY:

185994

show subpopulations

African (AFR)

AF:

0.0100

AC:

AN:

7900

American (AMR)

AF:

0.00804

AC:

150

AN:

18664

Ashkenazi Jewish (ASJ)

AF:

0.000918

AC:

AN:

11978

East Asian (EAS)

AF:

0.00909

AC:

225

AN:

24758

South Asian (SAS)

AF:

0.00962

AC:

259

AN:

26936

European-Finnish (FIN)

AF:

0.00514

AC:

109

AN:

21200

Middle Eastern (MID)

AF:

0.0139

AC:

AN:

1578

European-Non Finnish (NFE)

AF:

0.00904

AC:

1953

AN:

215952

Other (OTH)

AF:

0.00724

AC:

144

AN:

19888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

158

237

316

395

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00533

AC:

582

AN:

109112

Hom.:

Cov.:

AF XY:

0.00564

AC XY:

297

AN XY:

52640

show subpopulations

African (AFR)

AF:

0.00456

AC:

111

AN:

24346

American (AMR)

AF:

0.00319

AC:

AN:

10970

Ashkenazi Jewish (ASJ)

AF:

0.00176

AC:

AN:

2848

East Asian (EAS)

AF:

0.0123

AC:

AN:

3728

South Asian (SAS)

AF:

0.00693

AC:

AN:

3610

European-Finnish (FIN)

AF:

0.00261

AC:

AN:

6514

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.00609

AC:

333

AN:

54674

Other (OTH)

AF:

0.00494

AC:

AN:

1416

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

104

130

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

Alfa

AF:

0.00

Hom.:

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-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over