1-16996954-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022089.4(ATP13A2):c.1195+66A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 1,566,436 control chromosomes in the GnomAD database, including 530,914 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022089.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP13A2 | NM_022089.4 | c.1195+66A>G | intron_variant | Intron 12 of 28 | ENST00000326735.13 | NP_071372.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.807 AC: 122642AN: 152014Hom.: 49690 Cov.: 32
GnomAD4 exome AF: 0.824 AC: 1165591AN: 1414304Hom.: 481197 AF XY: 0.822 AC XY: 575821AN XY: 700902
GnomAD4 genome AF: 0.807 AC: 122716AN: 152132Hom.: 49717 Cov.: 32 AF XY: 0.807 AC XY: 60039AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 93. Only high quality variants are reported. -
Autosomal recessive spastic paraplegia type 78 Benign:1
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Kufor-Rakeb syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at