chr3-179148620-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006218.4(PIK3CA):c.-77+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,296 control chromosomes in the GnomAD database, including 2,841 homozygotes. 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 0.18 ( 2825 hom., cov: 32)
Exomes 𝑓: 0.25 ( 16 hom. )
Consequence
PIK3CA
NM_006218.4 intron
NM_006218.4 intron
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.886
Genes affected
PIK3CA (HGNC:8975): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) Phosphatidylinositol 3-kinase is composed of an 85 kDa regulatory subunit and a 110 kDa catalytic subunit. The protein encoded by this gene represents the catalytic subunit, which uses ATP to phosphorylate PtdIns, PtdIns4P and PtdIns(4,5)P2. This gene has been found to be oncogenic and has been implicated in cervical cancers. A pseudogene of this gene has been defined on chromosome 22. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3CA | NM_006218.4 | c.-77+17C>T | intron_variant | ENST00000263967.4 | |||
PIK3CA | XM_006713658.5 | c.-77+401C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CA | ENST00000263967.4 | c.-77+17C>T | intron_variant | 2 | NM_006218.4 | P1 | |||
PIK3CA | ENST00000477735.1 | c.-77+401C>T | intron_variant | 4 | |||||
PIK3CA | ENST00000643187.1 | c.-77+17C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.175 AC: 26634AN: 151804Hom.: 2822 Cov.: 32
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GnomAD4 exome AF: 0.250 AC: 94AN: 376Hom.: 16 Cov.: 0 AF XY: 0.248 AC XY: 65AN XY: 262
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GnomAD4 genome ? AF: 0.175 AC: 26644AN: 151920Hom.: 2825 Cov.: 32 AF XY: 0.172 AC XY: 12786AN XY: 74282
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
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