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GeneBe

22-45729600-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_013236.4(ATXN10):c.894+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,613,894 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0044 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0061 ( 34 hom. )

Consequence

ATXN10
NM_013236.4 intron

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.514
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 22-45729600-G-T is Benign according to our data. Variant chr22-45729600-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1285177.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr22-45729600-G-T is described in Lovd as [Likely_benign].
BS2
High AC in GnomAd at 675 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATXN10NM_013236.4 linkuse as main transcriptc.894+10G>T intron_variant ENST00000252934.10
ATXN10NM_001167621.2 linkuse as main transcriptc.702+10G>T intron_variant
ATXN10XM_047441314.1 linkuse as main transcriptc.894+10G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATXN10ENST00000252934.10 linkuse as main transcriptc.894+10G>T intron_variant 1 NM_013236.4 P1Q9UBB4-1

Frequencies

GnomAD3 genomes
AF:
0.00444
AC:
675
AN:
152130
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00347
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00186
Gnomad FIN
AF:
0.00359
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00756
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00423
AC:
1063
AN:
251280
Hom.:
5
AF XY:
0.00457
AC XY:
621
AN XY:
135804
show subpopulations
Gnomad AFR exome
AF:
0.000800
Gnomad AMR exome
AF:
0.00260
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00144
Gnomad FIN exome
AF:
0.00408
Gnomad NFE exome
AF:
0.00705
Gnomad OTH exome
AF:
0.00424
GnomAD4 exome
AF:
0.00608
AC:
8892
AN:
1461646
Hom.:
34
Cov.:
31
AF XY:
0.00614
AC XY:
4461
AN XY:
727124
show subpopulations
Gnomad4 AFR exome
AF:
0.000926
Gnomad4 AMR exome
AF:
0.00250
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00169
Gnomad4 FIN exome
AF:
0.00428
Gnomad4 NFE exome
AF:
0.00722
Gnomad4 OTH exome
AF:
0.00560
GnomAD4 genome
AF:
0.00442
AC:
673
AN:
152248
Hom.:
4
Cov.:
32
AF XY:
0.00406
AC XY:
302
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.00125
Gnomad4 AMR
AF:
0.00347
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00186
Gnomad4 FIN
AF:
0.00359
Gnomad4 NFE
AF:
0.00753
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00521
Hom.:
1
Bravo
AF:
0.00413
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Likely benign, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, University Medical Center Utrecht-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
1.4
Dann
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs141434930; hg19: chr22-46125480; API