ClinVar Miner

Submissions for variant NM_006218.4(PIK3CA):c.2015+9A>G

gnomAD frequency: 0.00032  dbSNP: rs200768351
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Brain Malformations Variant Curation Expert Panel RCV001836826 SCV001949975 likely benign Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes 2022-02-12 reviewed by expert panel curation The c.2015+9A>G (NM_006218.4) variant in PIK3CA is an intronic variant. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0008591 in the African/African American population, which is higher than the ClinGen BMEP threshold ([>0.00037]) for BS1, and therefore meets this criterion (BS1). The results from in silico splicing predictors MaxEntScan, spliceAI and varSEAK support that this variant does not affect splicing (BP4). This variant is a synonymous (silent) variant that occurs at a nucleotide that is not conserved according to a PhyloP <0.1 (BP7). In summary, this variant meets the criteria to be classified as Likely benign for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: BS1, BP4, BP7; -6 points (VCEP specifications version 1; Approved: 1/31/2021)
Invitae RCV000458168 SCV000554279 likely benign Cowden syndrome 2023-12-11 criteria provided, single submitter clinical testing
GeneDx RCV001672777 SCV001886249 benign not provided 2020-09-08 criteria provided, single submitter clinical testing

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