rs377365362

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_001195248.2(APTX):​c.*851_*852delCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 405,958 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 0 hom. )

Consequence

APTX
NM_001195248.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.100
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 Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 9-32972645-AAG-A is Benign according to our data. Variant chr9-32972645-AAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 366581.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00286 (436/152342) while in subpopulation AFR AF= 0.0102 (423/41570). AF 95% confidence interval is 0.00938. There are 1 homozygotes in gnomad4. There are 202 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
APTXNM_001195248.2 linkc.*851_*852delCT 3_prime_UTR_variant Exon 8 of 8 ENST00000379817.7 NP_001182177.2 Q7Z2E3-7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
APTXENST00000379817 linkc.*851_*852delCT 3_prime_UTR_variant Exon 8 of 8 1 NM_001195248.2 ENSP00000369145.2 Q7Z2E3-7

Frequencies

GnomAD3 genomes
AF:
0.00287
AC:
437
AN:
152224
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0102
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000589
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000732
AC:
70
AN:
95568
Hom.:
1
AF XY:
0.000560
AC XY:
29
AN XY:
51774
show subpopulations
Gnomad AFR exome
AF:
0.0109
Gnomad AMR exome
AF:
0.000476
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000704
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000335
AC:
85
AN:
253616
Hom.:
0
AF XY:
0.000279
AC XY:
40
AN XY:
143340
show subpopulations
Gnomad4 AFR exome
AF:
0.00990
Gnomad4 AMR exome
AF:
0.000428
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000504
GnomAD4 genome
AF:
0.00286
AC:
436
AN:
152342
Hom.:
1
Cov.:
32
AF XY:
0.00271
AC XY:
202
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.0102
Gnomad4 AMR
AF:
0.000588
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00143
Hom.:
0
Bravo
AF:
0.00301
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Coenzyme Q10 deficiency, Oculomotor Apraxia Type Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs377365362; hg19: chr9-32972643; API