rs3738814
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022089.4(ATP13A2):c.289-109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,514,810 control chromosomes in the GnomAD database, including 166,474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.52 ( 21091 hom., cov: 32)
Exomes 𝑓: 0.46 ( 145383 hom. )
Consequence
ATP13A2
NM_022089.4 intron
NM_022089.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0320
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 1-17005181-A-G is Benign according to our data. Variant chr1-17005181-A-G is described in ClinVar as [Benign]. Clinvar id is 1270274.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-17005181-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP13A2 | NM_022089.4 | c.289-109T>C | intron_variant | ENST00000326735.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP13A2 | ENST00000326735.13 | c.289-109T>C | intron_variant | 1 | NM_022089.4 | A1 | |||
ENST00000617114.5 | c.308-109T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.518 AC: 78651AN: 151868Hom.: 21041 Cov.: 32
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GnomAD4 exome AF: 0.457 AC: 622609AN: 1362826Hom.: 145383 Cov.: 22 AF XY: 0.459 AC XY: 313272AN XY: 681916
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GnomAD4 genome ? AF: 0.518 AC: 78756AN: 151984Hom.: 21091 Cov.: 32 AF XY: 0.525 AC XY: 39035AN XY: 74282
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 71% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 66. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at