Starting
Initialising…
0%
BRAF
Final classification
VUS
BRAF c.1796C>G · p.Thr599Arg
BRAF

The BRAF c.1796C>G (p.Thr599Arg) variant has been reported in ClinVar as pathogenic, including an expert panel pathogenic classification, and is also represented in curated cancer variant resources.

Gene
BRAF
Transcript
NM_001354609.1
HGVS · transcript:coding
NM_001354609.1:c.1796C>G
Consequence
N/A
GRCh38
chr7:140753339 G>C
GRCh37
chr7:140453139 G>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 was evaluated deterministically with applied criteria: PS3 moderate, PM1 moderate, PM2 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: PS3 moderate, PM1 moderate, PM2 supporting, PP5 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS3PM1PM2PP5 VUS
BRAF c.1796C>G

The BRAF c.1796C>G (p.Thr599Arg) variant has been reported in ClinVar as pathogenic, including an expert panel pathogenic classification, and is also represented in curated cancer variant resources.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, which supports rarity in population reference datasets.2 In approved functional studies, this variant was classified as pathogenic in both MEK activation and ERK activation assays, supporting abnormal MAPK pathway signaling consistent with the disease mechanism.3 In silico evidence does not meet the BRAF RASopathy thresholds for PP3 or BP4 because REVEL is 0.359, SpliceAI predicts no significant splice impact with a maximum delta score of 0.00, and BayesDel is 0.308415.4

PS3 + PM1 + PM2 + PP5 VUS
3 vcep_svi_rasopathy_vcep_v2_approved_functional_studiescspec ↗PMID:19206169 ↗
4 revelspliceai ↗bayesdelcspec ↗
Gene diagram · NM_001354609.1 · variants mapped to exon structure
BRAF NM_001354609.1
Fetching transcript structure from UCSC…
Applied criteria · 4 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 Pathogenic 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 = 0.00). REVEL score = 0.359. BayesDel score = 0.308415.
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: 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 previously been reported in somatic cancers (COSMIC; COSV56167356, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:19206169
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots