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PIK3R1
Final classification
VUS
PIK3R1 c.2079A>T · p.Glu693Asp
PIK3R1

NM_181523.2:c.2079A>T (p.Glu693Asp) is a missense variant in PIK3R1 that is absent from gnomAD v4.1, meeting PM2_Supporting under the ClinGen Antibody Deficiencies VCEP specifications (AF < 0.00000132).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.2079A>T
Consequence
N/A
GRCh38
chr5:68297505 A>T
GRCh37
chr5:67593333 A>T
Basis ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
PIK3R1 c.2079A>T

NM_181523.2:c.2079A>T (p.Glu693Asp) is a missense variant in PIK3R1 that is absent from gnomAD v4.1, meeting PM2_Supporting under the ClinGen Antibody Deficiencies VCEP specifications (AF < 0.00000132).1 The variant does not meet PP3 (REVEL 0.467 < 0.644 threshold) or BP4 (REVEL 0.467 > 0.290 threshold). SpliceAI predicts no splice impact (max delta = 0.00).2 No variant-specific functional data, de novo reports, co-segregation data, or proband phenotype data are available. The variant is absent from ClinVar and has not been reported in the literature.3 PVS1, PS1, PS2, PS3, PS4, PP1, PP3, PP4, BA1, BS1, BS3, BS4, BP4, BP5, and BP7 are not met. PM1, PM5, PM6 (use PS2 instead), PP2, PP5, BS2, BP1, BP2, and BP6 are not applicable under VCEP specifications.4 Total Bayesian points: +1 (PM2_Supporting). Under the Tavtigian et al. 2020 point scale adopted by the Antibody Deficiencies VCEP, 0–5 points corresponds to a classification of Uncertain Significance.5

PM2 VUS
2 revelspliceai ↗
3 clinvar ↗vcep_04_08_26_pik3r1_functional_assays_ps3_bs3
4 cspec ↗pvs1_variant_assessment
5 final_classification_frameworkvcep_bayesian_rules_variant_classification_pik3r1
Gene diagram · NM_181523.2 · variants mapped to exon structure
PIK3R1 NM_181523.2
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.467. BayesDel score = 0.0115145.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PIK3R1, the regulatory subunit of PI3-kinase, is mutated in various cancers, most frequently in glioma, endometrial and colorectal cancers.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots