9-32966630-A-T

Variant summary

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

The ENST00000672519.1(APTX):​n.*389-19012T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,242 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.040 ( 152 hom., cov: 32)

Consequence

APTX
ENST00000672519.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.21
Variant links:
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-32966630-A-T is Benign according to our data. Variant chr9-32966630-A-T is described in ClinVar as [Benign]. Clinvar id is 3256840.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APTXENST00000672519.1 linkn.*389-19012T>A intron_variant Intron 5 of 6 ENSP00000500320.1 Q7Z2E3-12
APTXENST00000672846.1 linkn.*923+46T>A intron_variant Intron 9 of 10 ENSP00000500396.1 Q7Z2E3-12

Frequencies

GnomAD3 genomes
AF:
0.0397
AC:
6037
AN:
152124
Hom.:
152
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0413
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.0581
Gnomad ASJ
AF:
0.0239
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.0396
Gnomad FIN
AF:
0.0333
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0297
Gnomad OTH
AF:
0.0401
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0397
AC:
6039
AN:
152242
Hom.:
152
Cov.:
32
AF XY:
0.0418
AC XY:
3115
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0413
Gnomad4 AMR
AF:
0.0581
Gnomad4 ASJ
AF:
0.0239
Gnomad4 EAS
AF:
0.113
Gnomad4 SAS
AF:
0.0398
Gnomad4 FIN
AF:
0.0333
Gnomad4 NFE
AF:
0.0296
Gnomad4 OTH
AF:
0.0397
Alfa
AF:
0.0323
Hom.:
10
Bravo
AF:
0.0417
Asia WGS
AF:
0.0750
AC:
260
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Jul 31, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 20% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 19. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
6.3
DANN
Benign
0.79

Splicing

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: rs80154620; hg19: chr9-32966628; API