rs2076600

chr1-17010896-G-Achr1-17010896-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022089.4(ATP13A2):c.10+833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,938 control chromosomes in the GnomAD database, including 8,832 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 0.33 (8832 hom., cov: 31)
• Consequence: ATP13A2 NM_022089.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

Genes affected

ATP13A2 (HGNC:30213): (ATPase cation transporting 13A2) This gene encodes a member of the P5 subfamily of ATPases which transports inorganic cations as well as other substrates. Mutations in this gene are associated with Kufor-Rakeb syndrome (KRS), also referred to as Parkinson disease 9. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP13A2	NM_022089.4	c.10+833C>T		intron_variant		ENST00000326735.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP13A2	ENST00000326735.13	c.10+833C>T		intron_variant		1	NM_022089.4	A1
ATP13A2	ENST00000341676.9	c.10+833C>T		intron_variant		1
ATP13A2	ENST00000452699.5	c.10+833C>T		intron_variant		1		P4
	ENST00000617114.5	c.29+833C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50281 AN: 151820 Hom.: 8814 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.328

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.331 AC: 50340 AN: 151938 Hom.: 8832 Cov.: 31 AF XY: 0.337 AC XY: 25045 AN XY: 74254

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.326

Alfa AF: 0.282 Hom.: 7546

Bravo AF: 0.342

Asia WGS AF: 0.388 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.5
Dann	Benign	0.90

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

Other links and lift over

dbSNP: rs2076600; hg19: chr1-17337391;