rs376189607
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_022089.4(ATP13A2):c.2610-9T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
ATP13A2
NM_022089.4 splice_polypyrimidine_tract, intron
NM_022089.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00009758
2
Clinical Significance
Conservation
PhyloP100: 1.22
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 1-16988483-A-G is Benign according to our data. Variant chr1-16988483-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 533809.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP13A2 | NM_022089.4 | c.2610-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000326735.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP13A2 | ENST00000326735.13 | c.2610-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_022089.4 | A1 | |||
ENST00000446261.1 | n.187+9371A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152174Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250318Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135590
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461018Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 726816
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GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Kufor-Rakeb syndrome;C5567893:Autosomal recessive spastic paraplegia type 78 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at