13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000673087.1(ENSG00000288330):n.48_49insCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG 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 0.0000092 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000086 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ENSG00000288330
ENST00000673087.1 non_coding_transcript_exon
ENST00000673087.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.36
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- spinocerebellar ataxia type 8Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ATXN8OS | NR_002717.3 | n.940_941insTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||
| ATXN8OS | NR_185834.1 | n.454-7926_454-7925insTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant | Intron 3 of 4 | ||||
| ATXN8OS | NR_185835.1 | n.454-7926_454-7925insTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant | Intron 3 of 6 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000288330 | ENST00000673087.1 | n.48_49insCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||||
| ATXN8OS | ENST00000756272.1 | n.813_814insTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||||
| ATXN8OS | ENST00000660386.1 | n.451-7926_451-7925insTGCTGCTGCAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC | intron_variant | Intron 3 of 3 |
Frequencies
GnomAD3 genomes 0.00000916 AC: 1AN: 109114Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
109114
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000859 AC: 3AN: 349206Hom.: 0 Cov.: 0 AF XY: 0.00000537 AC XY: 1AN XY: 186202 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
349206
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
186202
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
7906
American (AMR)
AF:
AC:
1
AN:
18694
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11978
East Asian (EAS)
AF:
AC:
0
AN:
24794
South Asian (SAS)
AF:
AC:
0
AN:
26972
European-Finnish (FIN)
AF:
AC:
0
AN:
21224
Middle Eastern (MID)
AF:
AC:
0
AN:
1578
European-Non Finnish (NFE)
AF:
AC:
0
AN:
216160
Other (OTH)
AF:
AC:
0
AN:
19900
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.018321), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.342
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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10
<30
30-35
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>80
Age
GnomAD4 genome 0.00000916 AC: 1AN: 109144Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 52666 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
109144
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
52666
show subpopulations
African (AFR)
AF:
AC:
1
AN:
24362
American (AMR)
AF:
AC:
0
AN:
10972
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2848
East Asian (EAS)
AF:
AC:
0
AN:
3730
South Asian (SAS)
AF:
AC:
0
AN:
3612
European-Finnish (FIN)
AF:
AC:
0
AN:
6518
Middle Eastern (MID)
AF:
AC:
0
AN:
236
European-Non Finnish (NFE)
AF:
AC:
0
AN:
54680
Other (OTH)
AF:
AC:
0
AN:
1416
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
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65-70
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>80
Age
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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