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RICTOR
Final classification
VUS
RICTOR c.3667G>T · p.Asp1223Tyr
RICTOR

NM_152756.4:c.3667G>T (p.Asp1223Tyr) is a missense variant in RICTOR. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).

Gene
RICTOR
Transcript
NM_152756.4
HGVS · transcript:coding
NM_152756.4:c.3667G>T
Consequence
N/A
GRCh38
chr5:38950181 C>A
GRCh37
chr5:38950283 C>A
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: PM2 supporting; combination = 1 supporting, 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: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
RICTOR c.3667G>T

NM_152756.4:c.3667G>T (p.Asp1223Tyr) is a missense variant in RICTOR. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).1 This variant is absent from ClinVar; no reputable source has classified it as pathogenic or benign. It is absent from COSMIC and does not lie in a statistically significant mutational hotspot.2 Computational predictors are equivocal: REVEL score is 0.471 (intermediate, below the typical 0.5 pathogenicity threshold), BayesDel is 0.102, and SpliceAI predicts no significant splice impact (max delta 0.05). These do not meet PP3 or BP4 thresholds.3 No variant-specific functional studies, segregation data, de novo reports, or case-control data are available. OncoKB reports Unknown Oncogenic Effect.4 Only one criterion is met: PM2 (supporting). Under the generic ACMG/AMP 2015 classification framework (PMID:25741868), a single supporting criterion is insufficient to classify this variant as likely pathogenic or likely benign. This variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 VUS
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_152756.4 · variants mapped to exon structure
RICTOR NM_152756.4
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 = 0.05). REVEL score = 0.471. BayesDel score = 0.102236.
      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. RICTOR, a core component of the oncogenic mTOR2 complex, is altered by amplification or mutation in various cancer types.
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots