22-45718267-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013236.4(ATXN10):c.648-146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 732,102 control chromosomes in the GnomAD database, including 12,074 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1978 hom., cov: 32)
Exomes 𝑓: 0.18 ( 10096 hom. )
Consequence
ATXN10
NM_013236.4 intron
NM_013236.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.549
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=-0.9).
BP6
?
Variant 22-45718267-C-T is Benign according to our data. Variant chr22-45718267-C-T is described in ClinVar as [Benign]. Clinvar id is 1296745.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN10 | NM_013236.4 | c.648-146C>T | intron_variant | ENST00000252934.10 | |||
ATXN10 | NM_001167621.2 | c.456-146C>T | intron_variant | ||||
ATXN10 | XM_047441314.1 | c.648-146C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN10 | ENST00000252934.10 | c.648-146C>T | intron_variant | 1 | NM_013236.4 | P1 | |||
ATXN10 | ENST00000381061.8 | c.456-146C>T | intron_variant | 2 | |||||
ATXN10 | ENST00000476998.5 | n.127-146C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ATXN10 | ENST00000498009.5 | n.822-146C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.142 AC: 21633AN: 151848Hom.: 1976 Cov.: 32
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GnomAD4 exome AF: 0.180 AC: 104552AN: 580136Hom.: 10096 AF XY: 0.178 AC XY: 56133AN XY: 314802
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GnomAD4 genome ? AF: 0.142 AC: 21637AN: 151966Hom.: 1978 Cov.: 32 AF XY: 0.144 AC XY: 10684AN XY: 74262
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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 submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at