ClinVar Miner

Submissions for variant NM_005027.4(PIK3R2):c.322+7A>G

gnomAD frequency: 0.00002  dbSNP: rs774883359
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Brain Malformations Variant Curation Expert Panel RCV001836919 SCV001949974 likely benign Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes 2022-02-11 reviewed by expert panel curation The c.322+7A>G (NM_005027.4) variant in PIK3R2 is an intronic variant. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0008153 in the Latino/Admixed 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 RCV002548233 SCV001091972 likely benign Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 2023-11-27 criteria provided, single submitter clinical testing

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