Genetic Variant ENSG00000288330:n.37_48dupCAGCAGCAGCAG (chr13-70139383-A-ACTGCTGCTGCTG) – 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.37_48dupCAGCAGCAGCAG 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 0.0065 ( 2 hom., cov: 0)

Exomes 𝑓: 0.0088 ( 313 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 710 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
ATXN8OS	NR_002717.3 link	n.929_940dupTGCTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	NR_185834.1 link	n.454-7937_454-7926dupTGCTGCTGCTGC	intron_variant	Intron 3 of 4
ATXN8OS	NR_185835.1 link	n.454-7937_454-7926dupTGCTGCTGCTGC	intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288330	ENST00000673087.1 link	n.37_48dupCAGCAGCAGCAG	non_coding_transcript_exon_variant	Exon 1 of 1
ATXN8OS	ENST00000756272.1 link	n.802_813dupTGCTGCTGCTGC	non_coding_transcript_exon_variant	Exon 5 of 5
ATXN8OS	ENST00000660386.1 link	n.451-7937_451-7926dupTGCTGCTGCTGC	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.00651

AC:

710

AN:

109090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00926

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00140

Gnomad EAS

AF:

0.0134

Gnomad SAS

AF:

0.00442

Gnomad FIN

AF:

0.00384

Gnomad MID

AF:

0.00781

Gnomad NFE

AF:

0.00631

Gnomad OTH

AF:

0.00710

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00879

AC:

3068

AN:

348980

Hom.:

313

Cov.:

AF XY:

0.00860

AC XY:

1600

AN XY:

186066

show subpopulations

African (AFR)

AF:

0.0159

AC:

126

AN:

7900

American (AMR)

AF:

0.00455

AC:

AN:

18676

Ashkenazi Jewish (ASJ)

AF:

0.00234

AC:

AN:

11976

East Asian (EAS)

AF:

0.0126

AC:

312

AN:

24770

South Asian (SAS)

AF:

0.00772

AC:

208

AN:

26938

European-Finnish (FIN)

AF:

0.00405

AC:

AN:

21218

Middle Eastern (MID)

AF:

0.00634

AC:

AN:

1578

European-Non Finnish (NFE)

AF:

0.00948

AC:

2048

AN:

216026

Other (OTH)

AF:

0.00829

AC:

165

AN:

19898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

170

254

339

424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.00651

AC:

710

AN:

109120

Hom.:

Cov.:

AF XY:

0.00661

AC XY:

348

AN XY:

52658

show subpopulations

African (AFR)

AF:

0.00928

AC:

226

AN:

24356

American (AMR)

AF:

0.00301

AC:

AN:

10970

Ashkenazi Jewish (ASJ)

AF:

0.00140

AC:

AN:

2848

East Asian (EAS)

AF:

0.0134

AC:

AN:

3724

South Asian (SAS)

AF:

0.00443

AC:

AN:

3612

European-Finnish (FIN)

AF:

0.00384

AC:

AN:

6514

Middle Eastern (MID)

AF:

0.00847

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.00631

AC:

345

AN:

54674

Other (OTH)

AF:

0.00636

AC:

AN:

1416

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

111

139

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-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

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