GeneBe

rs1554664711

Positions:

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001195248.2(APTX):​c.484-3_484-2insTGTTTTTTTTT variant causes a splice region, 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 0.00028 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00059 ( 3 hom. )

Consequence

APTX
NM_001195248.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.384
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6
Variant 9-32986032-T-TAAAAAAAAACA is Benign according to our data. Variant chr9-32986032-T-TAAAAAAAAACA is described in ClinVar as [Likely_benign]. Clinvar id is 2693722.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
APTXNM_001195248.2 linkuse as main transcriptc.484-3_484-2insTGTTTTTTTTT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000379817.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
APTXENST00000379817.7 linkuse as main transcriptc.484-3_484-2insTGTTTTTTTTT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_001195248.2 P1Q7Z2E3-7

Frequencies

GnomAD3 genomes
AF:
0.000278
AC:
4
AN:
14364
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000194
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00258
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000329
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000586
AC:
421
AN:
718738
Hom.:
3
Cov.:
10
AF XY:
0.000603
AC XY:
224
AN XY:
371534
show subpopulations
Gnomad4 AFR exome
AF:
0.00110
Gnomad4 AMR exome
AF:
0.00109
Gnomad4 ASJ exome
AF:
0.000434
Gnomad4 EAS exome
AF:
0.00196
Gnomad4 SAS exome
AF:
0.00161
Gnomad4 FIN exome
AF:
0.000457
Gnomad4 NFE exome
AF:
0.000391
Gnomad4 OTH exome
AF:
0.000629
GnomAD4 genome
AF:
0.000279
AC:
4
AN:
14360
Hom.:
0
Cov.:
0
AF XY:
0.000451
AC XY:
3
AN XY:
6650
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00260
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000330
Gnomad4 OTH
AF:
0.00

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 24, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs1554664711; hg19: chr9-32986030; API