Starting
Initialising…
0%
BRAF
Final classification
VUS
BRAF c.739T>C · p.Phe247Leu
BRAF

The BRAF c.739T>C (p.Phe247Leu) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as pathogenic, including by the ClinGen RASopathy Variant Curation Expert Panel.

Gene
BRAF
Transcript
NM_001354609.1
HGVS · transcript:coding
NM_001354609.1:c.739T>C
Consequence
N/A
GRCh38
chr7:140801533 A>G
GRCh37
chr7:140501333 A>G
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM1 moderate, PM2 supporting, PP2 supporting, PP3 supporting, PP5 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM1 moderate, PM2 supporting, PP2 supporting, PP3 supporting, PP5 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM1PM2PP2PP3PP5 VUS
BRAF c.739T>C

The BRAF c.739T>C (p.Phe247Leu) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as pathogenic, including by the ClinGen RASopathy Variant Curation Expert Panel.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, consistent with the BRAF RASopathy PM2_Supporting requirement for absence from population controls.2 This missense change lies in BRAF exon 6, a region specifically designated by the BRAF RASopathy specification as eligible for PM1.3 Computational evidence supports a deleterious effect, with REVEL 0.902 above the BRAF RASopathy PP3 threshold of 0.7, BayesDel 0.278133, and SpliceAI showing no meaningful splice impact with a maximum delta score of 0.10.4

PM1 + PM2 + PP2 + PP3 + PP5 VUS
Gene diagram · NM_001354609.1 · variants mapped to exon structure
BRAF NM_001354609.1
Fetching transcript structure from UCSC…
Applied criteria · 5 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 Pathogenic (4 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 180784)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.902. BayesDel score = 0.278133.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      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
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      28512244 ↗ Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. ONCOKB
      29533785 ↗ Systematic Functional Annotation of Somatic Mutations in Cancer. ONCOKB
      31515458 ↗ Response to Anti-EGFR Therapy in Patients with BRAF non-V600-Mutant Metastatic Colorectal Cancer. ONCOKB
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      20301303 ↗ Noonan Syndrome. CLINVAR
      20301365 ↗ PMID:20301365 CLINVAR
      20876176 ↗ Noonan syndrome: clinical features, diagnosis, and management guidelines. CLINVAR
      25173338 ↗ 2014 ESC Guidelines on diagnosis and management of hypertrophic cardiomyopathy: the Task Force for the Diagnosis and Management of Hypertrophic Cardiomyopathy of the European Society of Cardiology (ESC). CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR