rs200922655
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000379817.7(APTX):c.484-25_484-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,277,180 control chromosomes in the GnomAD database, including 14,600 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.42 ( 7125 hom., cov: 0)
Exomes 𝑓: 0.27 ( 7475 hom. )
Consequence
APTX
ENST00000379817.7 splice_region, splice_polypyrimidine_tract, intron
ENST00000379817.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.13
Genes affected
APTX (HGNC:15984): (aprataxin) This gene encodes a member of the histidine triad (HIT) superfamily. The encoded protein may play a role in single-stranded DNA repair through its nucleotide-binding activity and its diadenosine polyphosphate hydrolase activity. Mutations in this gene have been associated with ataxia-ocular apraxia. Alternatively spliced transcript variants have been identified for this gene.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 9-32986034-AAAAAAAAACAAAAAAAAAAAC-A is Benign according to our data. Variant chr9-32986034-AAAAAAAAACAAAAAAAAAAAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 198285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-32986034-AAAAAAAAACAAAAAAAAAAAC-A is described in Lovd as [Likely_benign]. Variant chr9-32986034-AAAAAAAAACAAAAAAAAAAAC-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APTX | NM_001195248.2 | c.484-25_484-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379817.7 | NP_001182177.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APTX | ENST00000379817.7 | c.484-25_484-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001195248.2 | ENSP00000369145 | P1 |
Frequencies
GnomAD3 genomes AF: 0.421 AC: 44470AN: 105626Hom.: 7126 Cov.: 0
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GnomAD4 exome AF: 0.266 AC: 311082AN: 1171552Hom.: 7475 AF XY: 0.261 AC XY: 152703AN XY: 586162
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GnomAD4 genome AF: 0.421 AC: 44465AN: 105628Hom.: 7125 Cov.: 0 AF XY: 0.416 AC XY: 21038AN XY: 50558
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 02, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 09, 2017 | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 11, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Mar 09, 2016 | - - |
Coenzyme Q10 deficiency, Oculomotor Apraxia Type Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at