rs16918936

chr9-33009029-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000468275.6(APTX):c.-5+15775A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,300 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.040 (150 hom., cov: 32)
• Consequence: APTX ENST00000468275.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• 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/exons	MANE	UniProt
APTX	NM_001368995.1	c.-5+15971A>C		intron_variant
APTX	NM_001368996.1	c.-5+15994A>C		intron_variant
APTX	NM_001368997.1	c.-5+15775A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APTX	ENST00000436040.7	c.-5+15994A>C		intron_variant		1
APTX	ENST00000468275.6	c.-5+15775A>C		intron_variant		1
APTX	ENST00000460940.6	c.-5+15971A>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6036 AN: 152182 Hom.: 150 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0395

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: 0.0396 AC: 6038 AN: 152300 Hom.: 150 Cov.: 32 AF XY: 0.0418 AC XY: 3112 AN XY: 74470

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0398

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0322 Hom.: 53

Bravo AF: 0.0418

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	7.3
Dann	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16918936; hg19: chr9-33009027;