chr5-103155798-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001276277.3(PPIP5K2):c.1404-111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 745,772 control chromosomes in the GnomAD database, including 30,396 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.24 ( 5041 hom., cov: 31)
Exomes 𝑓: 0.28 ( 25355 hom. )
Consequence
PPIP5K2
NM_001276277.3 intron
NM_001276277.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.130
Genes affected
PPIP5K2 (HGNC:29035): (diphosphoinositol pentakisphosphate kinase 2) This gene encodes a member of the histidine acid phosphatase family of proteins. Despite containing a histidine acid phosphatase domain, the encoded protein functions as an inositol pyrophosphate kinase, and is thought to lack phosphatase activity. This kinase activity is the mechanism by which the encoded protein synthesizes high-energy inositol pyrophosphates, which act as signaling molecules that regulate cellular homeostasis and other processes. This gene may be associated with autism spectrum disorder in human patients. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 5-103155798-A-G is Benign according to our data. Variant chr5-103155798-A-G is described in ClinVar as [Benign]. Clinvar id is 1237003.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPIP5K2 | NM_001276277.3 | c.1404-111A>G | intron_variant | ENST00000358359.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIP5K2 | ENST00000358359.8 | c.1404-111A>G | intron_variant | 1 | NM_001276277.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.236 AC: 35777AN: 151770Hom.: 5044 Cov.: 31
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GnomAD4 exome AF: 0.283 AC: 167933AN: 593886Hom.: 25355 AF XY: 0.277 AC XY: 88034AN XY: 318022
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GnomAD4 genome ? AF: 0.236 AC: 35787AN: 151886Hom.: 5041 Cov.: 31 AF XY: 0.235 AC XY: 17450AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at