GeneBe

rs60726084

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013236.4(ATXN10):​c.1174-11579_1174-11535delATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT variant causes a intron 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 DEL_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 0.000016 ( 0 hom., cov: 0)

Consequence

ATXN10
NM_013236.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

Publications

1 publications found
Variant links:
Genes affected
ATXN10 (HGNC:10549): (ataxin 10) This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]
ATXN10 Gene-Disease associations (from GenCC):
  • spinocerebellar ataxia type 10
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

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
ATXN10NM_013236.4 linkc.1174-11579_1174-11535delATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT intron_variant Intron 9 of 11 ENST00000252934.10 NP_037368.1 Q9UBB4-1
ATXN10NM_001167621.2 linkc.982-11579_982-11535delATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT intron_variant Intron 8 of 10 NP_001161093.1 Q9UBB4-2
ATXN10XM_047441314.1 linkc.1174-11579_1174-11535delATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT intron_variant Intron 9 of 11 XP_047297270.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATXN10ENST00000252934.10 linkc.1174-11604_1174-11560delATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT intron_variant Intron 9 of 11 1 NM_013236.4 ENSP00000252934.4 Q9UBB4-1

Frequencies

GnomAD3 genomes
AF:
0.0000158
AC:
2
AN:
126538
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000168
Gnomad OTH
AF:
0.000588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000158
AC:
2
AN:
126538
Hom.:
0
Cov.:
0
AF XY:
0.0000165
AC XY:
1
AN XY:
60720
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33232
American (AMR)
AF:
0.00
AC:
0
AN:
12334
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3076
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4038
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3626
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7936
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
0.0000168
AC:
1
AN:
59490
Other (OTH)
AF:
0.000588
AC:
1
AN:
1700
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
99

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs60726084; hg19: chr22-46191234; API