GeneBe

chr9-32986032-T-TAAAAAAAAACAAAA

Position:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001195248.2(APTX):​c.484-3_484-2insTTTTGTTTTTTTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000069 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00027 ( 4 hom. )

Consequence

APTX
NM_001195248.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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 -4 ACMG points.

BS2
High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
APTXNM_001195248.2 linkuse as main transcriptc.484-3_484-2insTTTTGTTTTTTTTT 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_484-2insTTTTGTTTTTTTTT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_001195248.2 P1Q7Z2E3-7

Frequencies

GnomAD3 genomes
AF:
0.0000695
AC:
1
AN:
14398
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:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000274
AC:
197
AN:
718818
Hom.:
4
Cov.:
10
AF XY:
0.000301
AC XY:
112
AN XY:
371572
show subpopulations
Gnomad4 AFR exome
AF:
0.000647
Gnomad4 AMR exome
AF:
0.000524
Gnomad4 ASJ exome
AF:
0.000372
Gnomad4 EAS exome
AF:
0.00115
Gnomad4 SAS exome
AF:
0.000718
Gnomad4 FIN exome
AF:
0.000105
Gnomad4 NFE exome
AF:
0.000179
Gnomad4 OTH exome
AF:
0.000189
GnomAD4 genome
AF:
0.0000695
AC:
1
AN:
14398
Hom.:
0
Cov.:
0
AF XY:
0.000150
AC XY:
1
AN XY:
6660
show subpopulations
Gnomad4 AFR
AF:
0.000194
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

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