rs754565169
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001195248.2(APTX):c.484-13delG variant causes a 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 intron
NM_001195248.2 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]
Genome browser will be placed here
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APTX | NM_001195248.2 | c.484-13delG | intron_variant | ENST00000379817.7 | NP_001182177.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APTX | ENST00000379817.7 | c.484-13delG | intron_variant | 1 | NM_001195248.2 | ENSP00000369145.2 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 47AN: 110118Hom.: 0 Cov.: 19
GnomAD3 genomes
AF:
AC:
47
AN:
110118
Hom.:
Cov.:
19
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000804 AC: 645AN: 802546Hom.: 8 Cov.: 16 AF XY: 0.000773 AC XY: 314AN XY: 406180
GnomAD4 exome
AF:
AC:
645
AN:
802546
Hom.:
Cov.:
16
AF XY:
AC XY:
314
AN XY:
406180
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000436 AC: 48AN: 110108Hom.: 0 Cov.: 19 AF XY: 0.000455 AC XY: 24AN XY: 52772
GnomAD4 genome
AF:
AC:
48
AN:
110108
Hom.:
Cov.:
19
AF XY:
AC XY:
24
AN XY:
52772
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Labcorp Genetics (formerly Invitae), Labcorp | Nov 01, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at