chr3-179198731-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006218.4(PIK3CA):c.-76-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 634,656 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0088 ( 42 hom., cov: 32)
Exomes 𝑓: 0.014 ( 256 hom. )
Consequence
PIK3CA
NM_006218.4 intron
NM_006218.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.27
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 3-179198731-T-C is Benign according to our data. Variant chr3-179198731-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1181592.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-179198731-T-C is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3CA | NM_006218.4 | c.-76-19T>C | intron_variant | ENST00000263967.4 | |||
PIK3CA | XM_006713658.5 | c.-76-19T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3CA | ENST00000263967.4 | c.-76-19T>C | intron_variant | 2 | NM_006218.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00882 AC: 1343AN: 152198Hom.: 42 Cov.: 32
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GnomAD4 exome AF: 0.0136 AC: 6555AN: 482340Hom.: 256 Cov.: 6 AF XY: 0.0133 AC XY: 3320AN XY: 249972
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GnomAD4 genome ? AF: 0.00879 AC: 1339AN: 152316Hom.: 42 Cov.: 32 AF XY: 0.00934 AC XY: 696AN XY: 74490
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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