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RAF1
Final classification
VUS
RAF1 c.1193G>T · p.Arg398Leu
RAF1

The RAF1 c.1193G>T (p.Arg398Leu) variant has been reported in ClinVar, where the ClinGen RASopathy Variant Curation Expert Panel classified it as uncertain significance and additional clinical laboratories have submitted both likely pathogenic and uncertain significance assertions.

Gene
RAF1
Transcript
NM_002880.4
HGVS · transcript:coding
NM_002880.4:c.1193G>T
Consequence
N/A
GRCh38
chr3:12591708 C>A
GRCh37
chr3:12633207 C>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAF1 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAF1 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP3 VUS
RAF1 c.1193G>T

The RAF1 c.1193G>T (p.Arg398Leu) variant has been reported in ClinVar, where the ClinGen RASopathy Variant Curation Expert Panel classified it as uncertain significance and additional clinical laboratories have submitted both likely pathogenic and uncertain significance assertions.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, consistent with PM2_Supporting under the RAF1 RASopathy specification.2 For this missense change, REVEL is 0.861, which exceeds the RAF1 PP3 threshold of 0.7; BayesDel is 0.342905; and SpliceAI predicts no significant splice effect with a maximum delta score of 0.10.3

PM2 + PP3 VUS
Gene diagram · NM_002880.4 · variants mapped to exon structure
RAF1 NM_002880.4
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.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Uncertain Significance by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.861. BayesDel score = 0.342905.
      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. RAF1 (CRAF), an intracellular kinase and component of the pro-oncogenic MAP-kinase signaling pathway, is infrequently mutated in cancer. Germline muta
      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 previously been reported in somatic cancers (COSMIC; COSV52583001, n = 4 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots