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LYFE SCIENCES
Project: HERA
NM_006218.2:c.2015+9A>G
p.?  ·  PIK3CA
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Classification rationale
1

The PIK3CA NM_006218.2:c.2015+9A>G (NP_006209.2:p.?) variant has been reported in ClinVar, where the aggregate classification is likely benign and the ClinGen Brain Malformations Variant Curation Expert Panel has classified it as likely benign.

clinvar ↗
2

This variant is present in population databases at a frequency above the Brain Malformations VCEP BS1 threshold of 0.0185%, including 31/249678 alleles in gnomAD v2.1 (AF 0.01242%) and a highest observed African/African American frequency of 0.09391% in gnomAD v4.1.

gnomad_v2 ↗ gnomad_v4 ↗
3

No variant-specific functional study was identified showing either an abnormal or a normal effect on PIK3CA splicing or function.

cspec ↗
4

Available computational splicing evidence could not be independently confirmed as a complete 2-of-3 benign prediction set, so BP4 and BP7 were not applied from the available records.

spliceai ↗ cspec ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.00012416; MAF= 0.01242%, 31/249678 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000859107; MAF= 0.08591%, 20/23280 alleles, homozygotes = 0); grpmax FAF= 0.00052743.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 5.80893e-05; MAF= 0.00581%, 90/1549338 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000939149; MAF= 0.09391%, 68/72406 alleles, homozygotes = 0); grpmax FAF= 0.00075934.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory) and as Benign (1 clinical laboratory) and as Likely benign by ClinGen Brain Malformations Variant Curation Expert Panel (expert panel).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
06
Cancer hotspots
No cancer hotspot summary recorded.