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BRAF
Final classification
VUS
BRAF c.1741A>T · p.Asn581Tyr
BRAF

NM_004333.6:c.1741A>T (p.Asn581Tyr) is a missense variant in exon 14 of BRAF, encoding a substitution at a highly conserved residue within the kinase domain.

Gene
BRAF
Transcript
NM_004333.6
HGVS · transcript:coding
NM_004333.6:c.1741A>T
Consequence
N/A
GRCh38
chr7:140754187 T>A
GRCh37
chr7:140453987 T>A
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: PM2 supporting, PP2 supporting, PP3 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: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP2PP3 VUS
BRAF c.1741A>T

NM_004333.6:c.1741A>T (p.Asn581Tyr) is a missense variant in exon 14 of BRAF, encoding a substitution at a highly conserved residue within the kinase domain. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at Supporting strength per the ClinGen RASopathy VCEP v2.3.0 (PM2_Supporting).1 BRAF exhibits strong constraint against missense variation in gnomAD (missense Z-score >3.09), and missense variants are a common mechanism of RASopathy, meeting PP2 at Supporting strength. The REVEL in silico prediction score is 0.978, exceeding the VCEP threshold of ≥0.7 for PP3 at Supporting strength. SpliceAI predicts no significant splicing impact (max delta = 0.07).2 N581Y has been observed as a somatic variant in multiple cancer types: colorectal cancer cell line HT55 (Seth 2009, PMID:19474002), melanoma cell line WM3912 (Hutchinson 2015, PMID:26084293), and in a cfDNA NSCLC cohort where it was identified as a novel activating mutation by Ba/F3 assay (Negrao 2020, PMID:32540409). N581Y is catalogued in COSMIC (COSV56062673, n=7). OncoKB classifies it as Likely Oncogenic with Likely Gain-of-function effect.3 No germline RASopathy probands, de novo occurrences, or family segregation data are available for this variant. VCEP-approved functional assays (BRAF Kinase Activity, MEK/ERK Activation Assays) have no data for N581Y. The N581 residue lies in a statistically significant hotspot, but is outside the VCEP-specified PM1 domains (P-loop AA 459-474 and CR3 activation segment AA 594-627); PM1 is not met.

PM2 + PP2 + PP3 VUS
Gene diagram · NM_004333.6 · variants mapped to exon structure
BRAF NM_004333.6
Fetching transcript structure from UCSC…
Applied criteria · 3 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 has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 3257913)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.978. BayesDel score = 0.579861.
      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 Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56062673, n = 7 times).
      Hotspots
      This variant lies 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 · 6 PMIDs not cited in assessment
      30224342 ↗ Impact of BRAF Mutation Class on Disease Characteristics and Clinical Outcomes in BRAF-mutant Lung Cancer. ONCOKB
      32540409 ↗ Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations. ONCOKB
      19276360 ↗ Antitumor efficacy of the novel RAF inhibitor GDC-0879 is predicted by BRAFV600E mutational status and sustained extracellular signal-regulated kinase/mitogen-activated protein kinase pathway suppression. ONCOKB
      19474002 ↗ Concomitant mutations and splice variants in KRAS and BRAF demonstrate complex perturbation of the Ras/Raf signalling pathway in advanced colorectal cancer. ONCOKB
      26084293 ↗ ERBB activation modulates sensitivity to MEK1/2 inhibition in a subset of driver-negative melanoma. ONCOKB
      15035987 ↗ Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. CLINVAR