rs754565169
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001195248.2(APTX):c.484-13del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., cov: 19)
Exomes 𝑓: 0.00080 ( 8 hom. )
Consequence
APTX
NM_001195248.2 splice_polypyrimidine_tract, intron
NM_001195248.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.353
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 9-32986042-AC-A is Benign according to our data. Variant chr9-32986042-AC-A is described in ClinVar as [Likely_benign]. Clinvar id is 402383.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-32986042-AC-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000804 (645/802546) while in subpopulation AFR AF= 0.0152 (242/15928). AF 95% confidence interval is 0.0136. There are 8 homozygotes in gnomad4_exome. There are 314 alleles in male gnomad4_exome subpopulation. Median coverage is 16. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APTX | NM_001195248.2 | c.484-13del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000379817.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APTX | ENST00000379817.7 | c.484-13del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001195248.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 47AN: 110118Hom.: 0 Cov.: 19
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GnomAD4 exome AF: 0.000804 AC: 645AN: 802546Hom.: 8 Cov.: 16 AF XY: 0.000773 AC XY: 314AN XY: 406180
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GnomAD4 genome ? AF: 0.000436 AC: 48AN: 110108Hom.: 0 Cov.: 19 AF XY: 0.000455 AC XY: 24AN XY: 52772
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely 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: Similar deletions very frequent in ExAC - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at