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GeneBe

22-45718518-G-T

Variant summary

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

The NM_013236.4(ATXN10):c.728+25G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,594,808 control chromosomes in the GnomAD database, including 100,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 14627 hom., cov: 31)
Exomes 𝑓: 0.34 ( 86077 hom. )

Consequence

ATXN10
NM_013236.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.14
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=-0.76).
BP6
Variant 22-45718518-G-T is Benign according to our data. Variant chr22-45718518-G-T is described in ClinVar as [Benign]. Clinvar id is 1250676.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATXN10NM_013236.4 linkuse as main transcriptc.728+25G>T intron_variant ENST00000252934.10
ATXN10NM_001167621.2 linkuse as main transcriptc.536+25G>T intron_variant
ATXN10XM_047441314.1 linkuse as main transcriptc.728+25G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATXN10ENST00000252934.10 linkuse as main transcriptc.728+25G>T intron_variant 1 NM_013236.4 P1Q9UBB4-1
ATXN10ENST00000381061.8 linkuse as main transcriptc.536+25G>T intron_variant 2 Q9UBB4-2
ATXN10ENST00000476998.5 linkuse as main transcriptn.207+25G>T intron_variant, non_coding_transcript_variant 3
ATXN10ENST00000483549.5 linkuse as main transcriptn.71+25G>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.414
AC:
62823
AN:
151866
Hom.:
14588
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.644
Gnomad AMI
AF:
0.321
Gnomad AMR
AF:
0.305
Gnomad ASJ
AF:
0.381
Gnomad EAS
AF:
0.277
Gnomad SAS
AF:
0.269
Gnomad FIN
AF:
0.324
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.337
Gnomad OTH
AF:
0.382
GnomAD3 exomes
AF:
0.329
AC:
82547
AN:
250626
Hom.:
14735
AF XY:
0.324
AC XY:
43865
AN XY:
135570
show subpopulations
Gnomad AFR exome
AF:
0.655
Gnomad AMR exome
AF:
0.258
Gnomad ASJ exome
AF:
0.363
Gnomad EAS exome
AF:
0.257
Gnomad SAS exome
AF:
0.276
Gnomad FIN exome
AF:
0.330
Gnomad NFE exome
AF:
0.328
Gnomad OTH exome
AF:
0.334
GnomAD4 exome
AF:
0.340
AC:
490337
AN:
1442824
Hom.:
86077
Cov.:
29
AF XY:
0.337
AC XY:
242514
AN XY:
718964
show subpopulations
Gnomad4 AFR exome
AF:
0.659
Gnomad4 AMR exome
AF:
0.265
Gnomad4 ASJ exome
AF:
0.365
Gnomad4 EAS exome
AF:
0.344
Gnomad4 SAS exome
AF:
0.275
Gnomad4 FIN exome
AF:
0.327
Gnomad4 NFE exome
AF:
0.337
Gnomad4 OTH exome
AF:
0.354
GnomAD4 genome
AF:
0.414
AC:
62919
AN:
151984
Hom.:
14627
Cov.:
31
AF XY:
0.410
AC XY:
30426
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.644
Gnomad4 AMR
AF:
0.304
Gnomad4 ASJ
AF:
0.381
Gnomad4 EAS
AF:
0.277
Gnomad4 SAS
AF:
0.270
Gnomad4 FIN
AF:
0.324
Gnomad4 NFE
AF:
0.337
Gnomad4 OTH
AF:
0.379
Alfa
AF:
0.363
Hom.:
3609
Bravo
AF:
0.422
Asia WGS
AF:
0.278
AC:
967
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 testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
5.9
Dann
Benign
0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs138156; hg19: chr22-46114398; COSMIC: COSV53294235; COSMIC: COSV53294235; API