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AKT1
Final classification
VUS
AKT1 c.235_238delinsAAGG · p.Gln79_Trp80delinsLysGly
AKT1

PM1 is met at moderate strength: the variant alters residues Gln79 and Trp80 within a statistically significant CancerHotspots mutational hotspot in the AKT1 PH domain, a critical functional region with no observed benign variation.

Gene
AKT1
Transcript
NM_001014431.1
HGVS · transcript:coding
NM_001014431.1:c.235_238delinsAAGG
Consequence
N/A
GRCh38
chr14:104776708 ACTG>CCTT
GRCh37
chr14:105243045 ACTG>CCTT
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
AKT1 c.235_238delinsAAGG

PM1 is met at moderate strength: the variant alters residues Gln79 and Trp80 within a statistically significant CancerHotspots mutational hotspot in the AKT1 PH domain, a critical functional region with no observed benign variation.1 PM2 is met at moderate strength: the variant is absent from all gnomAD populations (v2.1 exomes, v4.1 exomes, Canada genomes), with an allele frequency of 0.00%.2 Two moderate pathogenic criteria (PM1 + PM2) are insufficient to reach a likely pathogenic classification under generic ACMG/AMP 2015 combination rules (PMID:25741868), which require either 1 very strong + 1 moderate, or 1 strong + 2 moderate, or 2 moderate criteria. The variant is classified as a variant of uncertain significance (VUS).3 PVS1 is not applicable: Mutalyzer normalization resolves the variant to two adjacent missense substitutions (p.Q79K, p.W80G) rather than a null variant.4 PS3 (functional studies), PS4 (case-control), PP1 (cosegregation), and multiple other criteria could not be assessed due to absence of variant-specific data in ClinVar, gnomAD, COSMIC, and the literature.5

PM1 + PM2 VUS
Gene diagram · NM_001014431.1 · variants mapped to exon structure
AKT1 NM_001014431.1
Fetching transcript structure from UCSC…
Applied criteria · 2 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 = 0.06).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. AKT1, an intracellular kinase, is altered predominantly by mutation in various cancer types including breast and endometrial cancers.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots