Starting
Initialising…
0%
BRAF
Final classification
Likely Pathogenic
BRAF c.739T>G · p.Phe247Val
BRAF

The BRAF c.739T>G (p.Phe247Val) variant has not been observed in COSMIC and has been reported in ClinVar, where the overall classification is likely pathogenic with expert panel review.

Gene
BRAF
Transcript
NM_001354609.1
HGVS · transcript:coding
NM_001354609.1:c.739T>G
Consequence
N/A
GRCh38
chr7:140801533 A>C
GRCh37
chr7:140501333 A>C
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: matched Rule14 (2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting, PP5 supporting; maps to Likely Pathogenic.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule14 (2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting, PP5 supporting; maps to Likely Pathogenic.
Classification rationale
PM1PM2PM5PP3PP5 Likely Pathogenic
BRAF c.739T>G

The BRAF c.739T>G (p.Phe247Val) variant has not been observed in COSMIC and has been reported in ClinVar, where the overall classification is likely pathogenic with expert panel review.1 This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, which supports PM2 at supporting strength under the BRAF RASopathy specification.2 This missense variant lies in BRAF exon 6, a region explicitly designated by the RASopathy VCEP for PM1 application, and other pathogenic or likely pathogenic missense changes have been reported at the same codon 247, supporting PM5 at moderate strength.3 Computational evidence supports a deleterious missense effect because REVEL is 0.921, above the VCEP PP3 threshold of 0.7, BayesDel is positive at 0.434669, and SpliceAI shows only a possible splice signal with a max delta score of 0.20.4

PM1 + PM2 + PM5 + PP3 + PP5 Likely Pathogenic
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 · supports pathogenic
      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 has been reported in ClinVar as Pathogenic (2 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Likely pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 44830)
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.20). REVEL score = 0.921. BayesDel score = 0.434669.
      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. BRAF, an intracellular kinase, is frequently mutated in melanoma, thyroid and lung cancers among others.
      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
      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
      24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants. CLINVAR
      31785789 ↗ Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders. CLINVAR
      20301303 ↗ Noonan Syndrome. CLINVAR
      20301365 ↗ Cardiofaciocutaneous Syndrome. 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