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GeneBe

22-45700063-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_013236.4(ATXN10):c.392-219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 152,040 control chromosomes in the GnomAD database, including 245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.054 ( 245 hom., cov: 31)

Consequence

ATXN10
NM_013236.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.57
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BP6
Variant 22-45700063-T-C is Benign according to our data. Variant chr22-45700063-T-C is described in ClinVar as [Benign]. Clinvar id is 1225212.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATXN10NM_013236.4 linkuse as main transcriptc.392-219T>C intron_variant ENST00000252934.10
ATXN10NM_001167621.2 linkuse as main transcriptc.200-219T>C intron_variant
ATXN10XM_047441314.1 linkuse as main transcriptc.392-219T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATXN10ENST00000252934.10 linkuse as main transcriptc.392-219T>C intron_variant 1 NM_013236.4 P1Q9UBB4-1
ATXN10ENST00000381061.8 linkuse as main transcriptc.200-219T>C intron_variant 2 Q9UBB4-2
ATXN10ENST00000470722.1 linkuse as main transcriptn.351-219T>C intron_variant, non_coding_transcript_variant 3
ATXN10ENST00000498009.5 linkuse as main transcriptn.566-219T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0536
AC:
8145
AN:
151920
Hom.:
245
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0793
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0451
Gnomad ASJ
AF:
0.0612
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0309
Gnomad FIN
AF:
0.0654
Gnomad MID
AF:
0.0256
Gnomad NFE
AF:
0.0443
Gnomad OTH
AF:
0.0484
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0536
AC:
8154
AN:
152040
Hom.:
245
Cov.:
31
AF XY:
0.0543
AC XY:
4036
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.0793
Gnomad4 AMR
AF:
0.0451
Gnomad4 ASJ
AF:
0.0612
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.0311
Gnomad4 FIN
AF:
0.0654
Gnomad4 NFE
AF:
0.0444
Gnomad4 OTH
AF:
0.0479
Alfa
AF:
0.0494
Hom.:
28
Bravo
AF:
0.0535
Asia WGS
AF:
0.0170
AC:
59
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.11
Dann
Benign
0.15

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: rs9614506; hg19: chr22-46095943; API