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PIK3CA
Final classification
VUS
PIK3CA c.2016-11G>A · p.?
PIK3CA

NM_006218.4:c.2016-11G>A is an intronic variant in PIK3CA (intron 13, 11 bases upstream of exon 13). The variant has been observed at low frequency in population databases: 7/262,544 alleles in gnomAD v2.1 (AF 0.00267%) and 71/1,580,816 alleles in gnomAD v4.1 (AF 0.00449%), with no homozygotes.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.2016-11G>A
Consequence
N/A
GRCh38
chr3:179220975 G>A
GRCh37
chr3:178938763 G>A
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: no point-contributing criteria = 0 points, which maps to VUS.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: no point-contributing criteria = 0 points, which maps to VUS.
Classification rationale
VUS
PIK3CA c.2016-11G>A

NM_006218.4:c.2016-11G>A is an intronic variant in PIK3CA (intron 13, 11 bases upstream of exon 13). The variant has been observed at low frequency in population databases: 7/262,544 alleles in gnomAD v2.1 (AF 0.00267%) and 71/1,580,816 alleles in gnomAD v4.1 (AF 0.00449%), with no homozygotes.1 SpliceAI predicts no splicing impact (max delta score = 0.00), suggesting the intronic nucleotide substitution does not create or disrupt a splice site.2 This variant has been reported in ClinVar as Likely benign by a single clinical laboratory (Labcorp Genetics, SCV002406335) with review status 'criteria provided, single submitter.' No expert panel classifications are available.3 No functional studies, case reports, segregation data, or de novo observations have been published for this variant. All six associated ClinVar PMIDs are general practice guidelines or background reviews with no variant-specific evidence.4 Under the Brain Malformations VCEP (v1.1.0) Tavtigian point framework, no pathogenic criteria are met and no benign criteria are met. The total point score is 0, which falls within the VUS range (0 to 5 points).5 Multiple benign-suggesting criteria (BP4, BP7) could not be fully assessed due to missing computational data (varSEAK, MaxEntScan, PhyloP). If additional splicing prediction tools confirm no impact and PhyloP indicates low conservation, this variant may be reclassified toward likely benign.6

Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
Fetching transcript structure from UCSC…
Applied criteria · 0 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.49135e-05; MAF= 0.00449%, 71/1580816 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.58465e-05; MAF= 0.00558%, 65/1163904 alleles, homozygotes = 0); grpmax FAF= 4.489e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 2.66622e-05; MAF= 0.00267%, 7/262544 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 6.43501e-05; MAF= 0.00644%, 2/31080 alleles, homozygotes = 0); grpmax FAF= 1.277e-05.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0045% · 71 / 1,580,816
      0 hom · FAF 0.0045%
      European (non-Finnish)
      65 / 1,163,904
      0.0056%
      Admixed American
      3 / 55,214
      0.0054%
      Remaining individuals
      2 / 60,936
      0.0033%
      South Asian
      1 / 84,924
      0.0012%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0027% · 7 / 262,544
      0 hom · FAF 0.0013%
      Admixed American
      2 / 31,080
      0.0064%
      European (non-Finnish)
      5 / 121,974
      0.0041%
      + 6 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 1597494)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 6 PMIDs not cited in assessment
      23519317 ↗ Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR
      26389505 ↗ Genetics of Colorectal Cancer (PDQ®): Health Professional Version. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR