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BRAF
Final classification
VUS
BRAF c.1330C>T · p.Arg444Trp
BRAF

PM1 (Moderate) is met: variant c.1330C>T (p.Arg444Trp) is located in exon 11, a VCEP-designated critical functional domain for BRAF per RASopathy VCEP v2.3.0.

Gene
BRAF
Transcript
NM_004333.5
HGVS · transcript:coding
NM_004333.5:c.1330C>T
Consequence
N/A
GRCh38
chr7:140781678 G>A
GRCh37
chr7:140481478 G>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: PM1 moderate, PP2 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, PP2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM1PP2 VUS
BRAF c.1330C>T

PM1 (Moderate) is met: variant c.1330C>T (p.Arg444Trp) is located in exon 11, a VCEP-designated critical functional domain for BRAF per RASopathy VCEP v2.3.0.1 PP2 (Supporting) is met: BRAF gnomAD missense Z-score exceeds 3.09, indicating strong purifying selection against missense variation, consistent with a gene where missense variants are a common mechanism of RASopathy disease.2 PM2 is not met: the variant is present in gnomAD v2.1 (1/251,378) and v4.1 (1/1,613,628), which precludes application under the VCEP rule requiring absence from controls.3 PP3 is not met: REVEL score (0.637) falls below the VCEP PP3 threshold of ≥0.7, and SpliceAI (max delta 0.09) predicts no splicing impact.4 No benign criteria are met. BA1 and BS1 are not met (allele frequency far below population thresholds). BP4 is not met (REVEL 0.637 > 0.3 threshold).5 Under RASopathy VCEP v2.3.0 combination rules, PM1_Moderate + PP2_Supporting does not satisfy any Pathogenic, Likely Pathogenic, Benign, or Likely Benign rule. The minimum for Likely Pathogenic requires either 1 Strong + 1 Moderate, or ≥3 Moderate, or 1 Moderate + ≥4 Supporting criteria. Final classification: Variant of Uncertain Significance (VUS).6 PVS1, PS5, PP4, PP5, BS3, BP6 are not applicable under the VCEP framework. PS1, PS2, PS3, PS4, PM5, PM6, PP1, BS2, BS4, BP2, BP5 are not assessed due to absence of data. PM2, PP3, BA1, BS1, BP1, BP4, BP7 were assessed and not met.7 Three ClinVar-attached PMIDs (25394175, 31829902, 35924163) were reviewed in full text; none mention NM_004333.5:c.1330C>T or p.Arg444Trp. These papers are clinical practice guidelines or consensus statements on cancer genetics referral and prostate cancer biomarkers and do not provide variant-specific evidence.8

PM1 + PP2 VUS
Gene diagram · NM_004333.5 · variants mapped to exon structure
BRAF NM_004333.5
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
      This variant is present in gnomAD v4.1 (AF= 6.19722e-07; MAF= 0.00006%, 1/1613628 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66722e-05; MAF= 0.00167%, 1/59980 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.97807e-06; MAF= 0.00040%, 1/251378 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89235e-05; MAF= 0.00289%, 1/34574 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,613,628
      0 hom
      Admixed American
      1 / 59,980
      0.0017%
      + 9 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.0004% · 1 / 251,378
      0 hom
      Admixed American
      1 / 34,574
      0.0029%
      + 7 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.09). REVEL score = 0.637. BayesDel score = 0.25761.
      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. 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 previously been reported in somatic cancers (COSMIC; COSV56083156, n = 3 times).
      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 · 3 PMIDs not cited in assessment
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      31829902 ↗ Molecular Biomarkers in Localized Prostate Cancer: ASCO Guideline. CLINVAR
      35924163 ↗ Genetic Testing and Its Clinical Application in Prostate Cancer Management: Consensus Statements from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology. CLINVAR