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BRAF
Final classification
VUS
BRAF c.2107G>A · p.Glu703Lys
BRAF

NM_004333.5:c.2107G>A (p.Glu703Lys) is a missense variant in BRAF exon 17, within the C-terminal lobe of the kinase domain but outside all VCEP-specified PM1 critical functional domains (P-loop AA 459-474, CR3 activation segment AA 594-627).

Gene
BRAF
Transcript
NM_004333.5
HGVS · transcript:coding
NM_004333.5:c.2107G>A
Consequence
N/A
GRCh38
chr7:140739832 C>T
GRCh37
chr7:140439632 C>T
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; 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; no rule matched the adjudicated criteria.
Classification rationale
PM2PP2 VUS
BRAF c.2107G>A

NM_004333.5:c.2107G>A (p.Glu703Lys) is a missense variant in BRAF exon 17, within the C-terminal lobe of the kinase domain but outside all VCEP-specified PM1 critical functional domains (P-loop AA 459-474, CR3 activation segment AA 594-627).1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength under the RASopathy VCEP.2 BRAF has a gnomAD missense Z-score >3.09, meeting PP2 at supporting strength, consistent with low tolerance for benign missense variation in this gene.3 The REVEL score of 0.579 does not meet the VCEP thresholds for PP3 (≥0.7) or BP4 (≤0.3), and SpliceAI predicts no splice impact (max delta 0.06). Computational evidence is indeterminate.4 No functional data exists for p.Glu703Lys in any VCEP-approved assay (BRAF Kinase, MEK Activation, ERK Activation); the variant is not listed in the SVI functional studies spreadsheet. OncoKB reports Unknown Oncogenic Effect.5 No same-codon pathogenic comparator exists at residue 703 (PM5), no de novo observations have been reported (PS2/PM6), no case-control or segregation data is available (PS4/PP1), and no prior pathogenic assertion for E703K exists (PS1).6 ClinVar reports a single submitter classifying the variant as Uncertain Significance (Variation ID 4856330, criteria provided, single submitter). PP5 and BP6 are not applicable under this VCEP.7 The only met criteria are PM2_Supporting and PP2_Supporting. No pathogenic criteria at moderate, strong, or very strong level are met. Under the RASopathy VCEP combination rules, this evidence is insufficient to classify the variant as Pathogenic or Likely Pathogenic, and insufficient benign evidence exists to classify as Benign or Likely Benign. The variant remains a Variant of Uncertain Significance.8

PM2 + PP2 VUS
4 revelspliceai ↗
5 vcep_svi_rasopathy_vcep_v2_approved_functional_studiesoncokb ↗
6 clinvar ↗pm5_candidates
Gene diagram · NM_004333.5 · variants mapped to exon structure
BRAF NM_004333.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 16 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0, meeting the VCEP PM2_Supporting rule requiring absence from population controls.
Absent from gnomAD v2.1.Absent from gnomAD v4.1.Absent from gnomAD-Canada v1.0.
PP2 supporting Pathogenic
BRAF has a gnomAD missense Z-score >3.09, meeting the VCEP PP2 rule. BRAF is a well-established gene with low tolerance for benign missense variation, and missense variants are a common mechanism of disease in RASopathies.
BRAF gnomAD missense Z-score exceeds 3.09 (gene is highly constrained for missense variation).
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change to have been previously established as pathogenic.
PS2 No de novo occurrence of NM_004333.5:c.2107G>A has been reported.
PS3 No functional data exists for p.Glu703Lys in any VCEP-approved assay (BRAF Kinase Activity, MEK Activation Assay, ERK Activation Assay).
PS4 No case-control data or proband counts are available for NM_004333.5:c.2107G>A.
PM1 PM1 under the RASopathy VCEP is restricted to exon 6, exon 11, the P-loop (amino acids 459-474), and the CR3 activation segment (amino acids 594-627).
PM5 PM5 under the RASopathy VCEP requires at least one [likely] pathogenic residue change at the same codon.
PM6 No assumed de novo observation (without confirmed parentage) has been reported for NM_004333.5:c.2107G>A.
PP1 No co-segregation data is available for NM_004333.5:c.2107G>A.
PP3 The REVEL score for this variant is 0.579, below the VCEP PP3 threshold of REVEL ≥0.7.
Benign
BA1 BA1 under the RASopathy VCEP requires a gnomAD filtering allele frequency ≥0.05%.
BS1 BS1 under the RASopathy VCEP requires a gnomAD filtering allele frequency ≥0.025%.
BS2 No observations of this variant in healthy adult individuals have been reported.
BS4 No segregation data is available to demonstrate lack of segregation in affected family members.
BP2 No evidence of an alternative molecular cause of a RASopathy in the same gene has been identified.
BP4 BP4 under the RASopathy VCEP requires a REVEL score ≤0.3 for missense variants.
BP5 No evidence of an alternative molecular cause of a RASopathy in a different gene has been identified.
N/A · 10 PVS1 · PM3 · PM4 · PP4 · PP5 · BS3 · BP1 · BP3 · BP6 · BP7
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
Error retrieving ClinVar entry.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06). REVEL score = 0.579. BayesDel score = 0.0458388.
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 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 · 1 PMID not cited in assessment
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