13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000414504.6(ATXN8OS):​n.1146_1148delTGC variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 454,152 control chromosomes in the GnomAD database, including 199 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.025 ( 33 hom., cov: 0)
Exomes 𝑓: 0.024 ( 166 hom. )

Consequence

ATXN8OS
ENST00000414504.6 splice_region, non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATXN8OSNR_002717.3 linkn.938_940delTGC non_coding_transcript_exon_variant 5/5
ATXN8OSNR_185834.1 linkn.454-7928_454-7926delTGC intron_variant
ATXN8OSNR_185835.1 linkn.454-7928_454-7926delTGC intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATXN8OSENST00000414504.6 linkn.1146_1148delTGC splice_region_variant, non_coding_transcript_exon_variant 5/55
ENSG00000288330ENST00000673087.1 linkn.46_48delCAG non_coding_transcript_exon_variant 1/1
ATXN8OSENST00000660386.1 linkn.451-7928_451-7926delTGC intron_variant

Frequencies

GnomAD3 genomes
AF:
0.0250
AC:
2729
AN:
108972
Hom.:
33
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0261
Gnomad AMI
AF:
0.0195
Gnomad AMR
AF:
0.0271
Gnomad ASJ
AF:
0.0102
Gnomad EAS
AF:
0.0208
Gnomad SAS
AF:
0.0595
Gnomad FIN
AF:
0.0118
Gnomad MID
AF:
0.0508
Gnomad NFE
AF:
0.0244
Gnomad OTH
AF:
0.0278
GnomAD4 exome
AF:
0.0235
AC:
8119
AN:
345150
Hom.:
166
AF XY:
0.0243
AC XY:
4461
AN XY:
183850
show subpopulations
Gnomad4 AFR exome
AF:
0.0303
Gnomad4 AMR exome
AF:
0.0143
Gnomad4 ASJ exome
AF:
0.00843
Gnomad4 EAS exome
AF:
0.0296
Gnomad4 SAS exome
AF:
0.0420
Gnomad4 FIN exome
AF:
0.0147
Gnomad4 NFE exome
AF:
0.0227
Gnomad4 OTH exome
AF:
0.0234
GnomAD4 genome
AF:
0.0251
AC:
2731
AN:
109002
Hom.:
33
Cov.:
0
AF XY:
0.0250
AC XY:
1313
AN XY:
52588
show subpopulations
Gnomad4 AFR
AF:
0.0260
Gnomad4 AMR
AF:
0.0271
Gnomad4 ASJ
AF:
0.0102
Gnomad4 EAS
AF:
0.0209
Gnomad4 SAS
AF:
0.0599
Gnomad4 FIN
AF:
0.0118
Gnomad4 NFE
AF:
0.0244
Gnomad4 OTH
AF:
0.0290

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.

Other links and lift over

dbSNP: rs193922930; hg19: chr13-70713515; API