22-21483071-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NR_003700.1(PI4KAP2):n.964G>A variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. 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 0.000030 ( 0 hom., cov: 16)
Exomes 𝑓: 0.000017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PI4KAP2
NR_003700.1 non_coding_transcript_exon
NR_003700.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.35
Genes affected
PI4KAP2 (HGNC:33577): (phosphatidylinositol 4-kinase alpha pseudogene 2) Predicted to enable 1-phosphatidylinositol 4-kinase activity. Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and phosphatidylinositol-mediated signaling. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PI4KAP2 | NR_003700.1 | n.964G>A | non_coding_transcript_exon_variant | 8/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PI4KAP2 | ENST00000360806.9 | n.673G>A | non_coding_transcript_exon_variant | 6/16 | |||||
ENST00000450651.5 | n.1054G>A | non_coding_transcript_exon_variant | 8/17 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000297 AC: 4AN: 134606Hom.: 0 Cov.: 16
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GnomAD3 exomes AF: 0.0000188 AC: 3AN: 159696Hom.: 0 AF XY: 0.0000237 AC XY: 2AN XY: 84418
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000174 AC: 23AN: 1321968Hom.: 0 Cov.: 24 AF XY: 0.0000168 AC XY: 11AN XY: 654310
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GnomAD4 genome ? AF: 0.0000297 AC: 4AN: 134606Hom.: 0 Cov.: 16 AF XY: 0.0000154 AC XY: 1AN XY: 64748
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at