9-32891932-T-C

Variant summary

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

The ENST00000672846.1(APTX):​n.*1056-4686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,056 control chromosomes in the GnomAD database, including 36,392 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 36392 hom., cov: 32)

Consequence

APTX
ENST00000672846.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.239
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=-0.91).
BP6
Variant 9-32891932-T-C is Benign according to our data. Variant chr9-32891932-T-C is described in ClinVar as [Benign]. Clinvar id is 3256851.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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
APTXENST00000672846.1 linkn.*1056-4686A>G intron_variant Intron 10 of 10 ENSP00000500396.1 Q7Z2E3-12

Frequencies

GnomAD3 genomes
AF:
0.685
AC:
104044
AN:
151938
Hom.:
36372
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.643
Gnomad AMI
AF:
0.748
Gnomad AMR
AF:
0.604
Gnomad ASJ
AF:
0.668
Gnomad EAS
AF:
0.311
Gnomad SAS
AF:
0.701
Gnomad FIN
AF:
0.669
Gnomad MID
AF:
0.687
Gnomad NFE
AF:
0.757
Gnomad OTH
AF:
0.705
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.685
AC:
104124
AN:
152056
Hom.:
36392
Cov.:
32
AF XY:
0.676
AC XY:
50233
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.643
Gnomad4 AMR
AF:
0.604
Gnomad4 ASJ
AF:
0.668
Gnomad4 EAS
AF:
0.311
Gnomad4 SAS
AF:
0.703
Gnomad4 FIN
AF:
0.669
Gnomad4 NFE
AF:
0.757
Gnomad4 OTH
AF:
0.700
Alfa
AF:
0.718
Hom.:
4913
Bravo
AF:
0.675
Asia WGS
AF:
0.524
AC:
1823
AN:
3476

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 78% 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: 73. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.3
DANN
Benign
0.75

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: rs10115224; hg19: chr9-32891930; COSMIC: COSV60352196; API