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

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.

Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.2016-11G>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 applied · 12 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 0

No criteria were applied for this variant.

Assessed · not applied · 11 not met · 1 not assessed
Pathogenic
PS2 No de novo observations have been reported for this variant.
PS3 No well-established in vitro or in vivo functional studies have been performed for this variant.
PS4 No affected individuals with this variant have been reported in the literature or ClinVar with phenotype data suitable for VCEP Table 2A point assignment.
PM2 This variant is present in gnomAD at frequencies exceeding the VCEP PM2 threshold of ≤1 individual.
Benign
BA1 The allele frequency in gnomAD (0.0045% in v4.1) is well below the VCEP BA1 threshold of >0.0926%.
BS1 The allele frequency in gnomAD (0.0045% in v4.1) is below the VCEP BS1 threshold of >0.0185%.
BS2 No homozygotes are present in gnomAD (0 in both v2.1 and v4.1), and no well-phenotyped heterozygous family members have been reported.
BS3 No well-established in vitro or in vivo functional studies have been performed demonstrating no damaging effect on protein function or splicing for this variant.
BP2 No evidence is available indicating this variant has been observed in cis or trans with a known pathogenic variant in PIK3CA.
BP4 This intronic variant is eligible for BP4 assessment per VCEP rules, and SpliceAI predicts no splicing impact (max delta = 0.00).
BP5 No evidence is available indicating this variant was found in a case with an alternate molecular basis for disease.
BP7 This intronic variant is eligible for BP7 per VCEP rules, but no PhyloP conservation score is available to determine whether the nucleotide is non-conserved (PhyloP < 0.1 required).
N/A · 13 PVS1 · PS1 · PM1 · PM5 · PM6 · PP1 · PP2 · PP3 · PP4 · PP5 · BS4 · BP1 · BP6
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