Variant classification summary

NM_006218.4:c.2850A>G

PIK3CA · NP_006209.2:p.(Glu950=) · NM_006218.4

GRCh37: chr3:178948078 A>G · GRCh38: chr3:179230290 A>G

Gene: PIK3CA Transcript: NM_006218.4

Final call

VUS

PM1 supporting PM2 supporting

Variant details

Gene

PIK3CA

Transcript

NM_006218.4

Protein

NP_006209.2:p.(Glu950=)

gnomAD AF

6.20440537599317e-07 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006218.4:c.2850A>G (p.Glu950=) is a synonymous variant in PIK3CA exon 20. The ClinGen Brain Malformations VCEP (v1.1) framework was applied for criterion adjudication.

2

The variant falls within the C-terminal kinase domain (AA 797-1068), a Table 4 critical functional domain for PIK3CA per the VCEP specification, meeting PM1 at Supporting strength.

3

The variant is extremely rare in population databases: gnomAD v2.1 AF=0.00080% (2/248,508 alleles), gnomAD v4.1 AF=0.00006% (1/1,611,758 alleles), with zero homozygotes. PM2 is met at Supporting strength under VCEP rules.

4

PVS1, PS1, PM5, PM6, PP1, PP2, PP3, PP4, PP5, BS4, BP1, BP6, and BP3 are not applicable under the VCEP framework or due to the synonymous nature of the variant.

5

SpliceAI predicts no significant splicing impact (max delta=0.05), but BP4 requires two of three tools (varSEAK, SpliceAI, MaxEntScan) per VCEP specifications; only SpliceAI is available. BP7 requires a PhyloP score <0.1, which is not available. Both BP4 and BP7 remain not assessed.

6

No functional studies, de novo reports, case observations, or segregation data were identified for this synonymous variant. PS2, PS3, PS4, BS2, BS3, BP2, and BP5 are not met.

7

With PM1_Supporting (+1) and PM2_Supporting (+1), the total points sum to +2. Per the VCEP Tavtigian point-combination framework (Pathogenic ≥10, Likely Pathogenic 6-9, VUS 0-5, Likely Benign -6 to -1, Benign <-6), a score of +2 falls within the VUS (0-5) range.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PVS1 is not applicable because the disease mechanism for PIK3CA-related brain malformations is gain of function, not loss of function or haploinsufficiency.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PS1	N/A	PS1 requires the same amino acid change as a previously established pathogenic variant. This variant (NM_006218.4:c.2850A>G) is synonymous (p.Glu950=) and does not alter the amino acid; there is no amino acid change to compare.	cspec
PS2	Not met	VCEP PS2 requires de novo evidence with confirmed maternity/paternity plus tissue differential allele fraction (strong) or at minimum criterion 1 alone (moderate). No de novo data are available for this variant in the case materials or literature. The ClinVar submission from Ambry Genetics (SCV002749861) is germline origin but provides no de novo confirmation.	clinvar cspec
PS3	Not met	No functional studies were identified for NM_006218.4:c.2850A>G, a synonymous variant. OncoKB lists this variant as 'Unknown Oncogenic Effect' with no curated PMIDs. The reviewed publications (PMID:23619275, PMID:25730230) are policy statements about carrier screening that do not address PIK3CA functional data. No variant-specific or systematic-range functional characterization is available.	oncokb
PS4	Not met	VCEP PS4 requires phenotype point assignment (Tables 2A/2B) and is dependent on PM2 being met first for absent/rare in controls. No case reports of this variant in individuals with brain malformations were identified in the literature or ClinVar submissions. The variant has not been reported in COSMIC. Without affected case data, no PS4 points can be assigned.	clinvar cspec
PS5	N/A	PS5 is not a standard ACMG/AMP criterion. The ACMG 2015 guidelines define criteria PVS1, PS1-PS4, PM1-PM6, PP1-PP5. No PS5 criterion exists in the framework.
PM1	Met	Residue 950 (Glu950) falls within the C-terminal kinase domain (AA 797-1068) defined in Table 4 of the ClinGen Brain Malformations VCEP specification (v1.1) as a critical functional domain for PIK3CA. Under this VCEP, PM1 is awarded at Supporting strength for residues located within approved Table 4 domains, independent of hotspot recurrence.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PM2	Met	This variant is extremely rare in population databases. In gnomAD v2.1, it is present at AF=0.00080% (2/248,508 alleles) and in gnomAD v4.1 at AF=0.00006% (1/1,611,758 alleles), with zero homozygotes in both datasets. The highest subpopulation frequency is 0.00177% in European (non-Finnish) in v2.1. Under the VCEP, PM2 is awarded at Supporting strength for variants absent or rare (≤1 person) in ethnically-matched controls. The pooled allele count across datasets supports PM2 at supporting level.	gnomad_v2 gnomad_v4 cspec
PM5	N/A	PM5 is defined as a novel missense change at an amino acid residue where a different pathogenic missense change has been reported. This variant is synonymous (p.Glu950=), not missense. The pm5_candidates assessment confirms the variant class is not missense-like and is ineligible for classic PM5.	pm5_candidates cspec
PM6	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PM6 is not applicable because this point is addressed according to PS2 and will not be used.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PP1	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PP1 is not applicable since disease-causing variants are germline mosaic, de novo, or mosaic.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PP2	N/A	PP2 is defined in the original ACMG/AMP framework as a missense variant in a gene with a low rate of benign missense variation. This variant is synonymous (p.Glu950=), not missense. The VCEP rule uses missense constraint z-score, which is applicable to missense variant evaluation, not synonymous changes.	cspec
PP3	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PP3 is not applicable since these variants are gain-of-function and traditional mutation pathogenicity prediction algorithms focus on loss-of-function mechanisms.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PP4	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PP4 is not applicable since this criterion is accounted for under PS4.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PP5	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that PP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
BA1	Not met	VCEP BA1 threshold is allele frequency >0.0926%. The maximum observed population frequency for this variant is 0.00177% (European non-Finnish, gnomAD v2.1), which is approximately 50-fold below the BA1 threshold. This variant does not meet the stand-alone benign allele frequency criterion.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	VCEP BS1 threshold is allele frequency >0.0185%. The maximum observed population frequency for this variant is 0.00177% (European non-Finnish, gnomAD v2.1), which is approximately 10-fold below the BS1 threshold. This variant does not meet the strong benign allele frequency criterion.	gnomad_v2 gnomad_v4 cspec
BS2	Not met	VCEP BS2 requires ≥3 homozygotes in gnomAD or ≥3 heterozygous in well-phenotyped family members. This variant has zero homozygotes in both gnomAD v2.1 and v4.1. No well-phenotyped family member data are available in the case materials.	gnomad_v2 gnomad_v4 cspec
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing exist for this variant. OncoKB lists this variant as 'Unknown Oncogenic Effect' with no curated PMIDs. The reviewed publications (PMID:23619275, PMID:25730230) are policy statements unrelated to PIK3CA functional biology.	oncokb
BS4	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that BS4 is not applicable as these are de novo, germline mosaic, or post-zygotic mutations.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
BP1	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that BP1 is not applicable because loss of function is not the disease mechanism for PIK3CA.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
BP2	Not met	BP2 requires observation of this variant in cis or trans with a known pathogenic variant in the same gene. No such co-occurrence data are available in the case materials, ClinVar submissions, or reviewed literature.	cspec
BP4	Not assessed	VCEP BP4 requires two out of three splicing prediction tools (varSEAK, SpliceAI, MaxEntScan) to predict no impact on splicing. Only SpliceAI data is available (max delta = 0.05, indicating no significant splice impact). Without varSEAK and MaxEntScan scores, the criterion cannot be fully assessed. SpliceAI alone suggests no splicing effect, but this is insufficient to meet the VCEP's 2-of-3 tool requirement.	spliceai cspec
BP5	Not met	BP5 requires evidence that the variant is found in a case with an alternate molecular basis for disease. No such evidence is available for this variant in the case materials or literature.	cspec
BP6	N/A	The ClinGen Brain Malformations VCEP (v1.1) states that BP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
BP7	Not assessed	VCEP BP7 is applicable to synonymous variants and requires a PhyloP score <0.1 indicating the nucleotide is non-conserved. This is a synonymous variant (p.Glu950=) but the PhyloP conservation score is not available in the prefetch, evidence_brief, or any other case output. Without the PhyloP score, BP7 cannot be assessed.	cspec

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