The BRAF NM_004333.6:c.1790T>G (NP_004324.2:p.(Leu597Arg)) missense variant has previously been reported in somatic cancers (COSMIC; COSV56121113, n = 37 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: P.L597R increased both phospho-MEK and phospho-ERK in cells, representing two distinct VCEP-approved pathway assay types. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.BRAF encodes a protein kinase that helps control the MAPK/ERK signaling pathway, which regulates cell growth, division, and specialization. Changes in BRAF are associated with cardiofaciocutaneous, Noonan, and Costello syndromes. BRAF is an oncogene, and abnormal activation of its signaling can drive cancers including melanoma, thyroid cancer, colorectal cancer, lung cancer, lymphoma, and hairy cell leukemia.
The recorded framework is ClinGen BRAF VCEP v2.3. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, Moderate: p.L597R increased both phospho-MEK and phospho-ERK in cells, representing two distinct VCEP-approved pathway assay types.
Met at Moderate: residue 597 lies within the VCEP-defined CR3 activation segment, amino acids 594-627.
Met at Supporting: REVEL score 0.964 meets the BRAF VCEP missense threshold of ≥0.7.
No benign criterion marked as applied in the recorded assessment.
VUS: PS3 (moderate), PM1 (moderate), and PP3 (supporting) do not satisfy a BRAF VCEP pathogenic or benign combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 1 / 1,612,712 alleles. Recorded AF 6.20074e-07. Recorded homozygote count 0.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.964. Refer to the recorded PP3/BP4 rationale for interpretation.
A ClinVar laboratory submission summary was not recorded. ClinVar API review status: no assertion criteria provided.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV56121113, n = 37 times).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRAF VCEP v2.3, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 4 not met · 11 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
No proband-level de novo, parental-testing, affected-family segregation, non-segregation, or informative-meiosis evidence was available for these four criteria.
Accordingly, PS2, PM6, PP1, and BS4 are not_assessed rather than met or not_met.
Only PS4, PP4, PP5, BP5, and BP6 were adjudicated.
PS4 remains not_assessed because the available sources do not provide verified germline RASopathy case-control counts, a computable OR/RR with confidence interval, or sufficient unrelated affected probands for VCEP point scoring.
PP4, PP5, and BP6 are not applicable by explicit BRAF VCEP rules; BP5 remains not_assessed because no alternative molecular cause or fully explanatory alternate diagnosis is documented.
PP3 is met at Supporting from the VCEP-named missense REVEL path (0.964 ≥ 0.7).
BP4 is not met because the VCEP-named missense REVEL score (0.964) is above 0.3.
BP7 is not applicable because the variant is missense and outside BP7's stated synonymous, noncanonical intronic, and non-coding scope.
No criteria match.
PS3 is met at Moderate strength. The VCEP rule specifies Moderate strength for "Two or more different approved assays." The variant-specific study PMID:22798288 tested ectopically expressed BRAF p.L597R in 293H cells and showed increased phospho-MEK and phospho-ERK relative to vector control, with suppression by vemurafenib and GSK1120212. These are two distinct approved pathway assay types in the governing functional-studies file: MEK Activation Assay, which measures the phosphorylated-to-unphosphorylated MEK ratio, and ERK Activation Assay, which measures the phosphorylated-to-unphosphorylated ERK ratio. The study used engineered, sequence-confirmed BRAF constructs and included vector and wild-type/activating-mutant comparison context, but the extracted publication does not establish the full VCEP assay-validation package or report independent biological replicate details; therefore human review is warranted for the Moderate upgrade. The governing functional-studies table was searched for c.1790T>G, p.Leu597Arg, and p.L597R and contains no variant-specific entry or pre-assigned code for this variant.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Approved assays are available in the supplemental materials. ... Two or more different approved assays.
The variant changes BRAF residue 597. The BRAF VCEP defines the CR3 activation segment as amino acids 594-627, so residue 597 lies within the VCEP-approved critical and well-established functional domain. The authoritative domain_tables entry for BRAF is empty, so the VCEP CSPEC domain definition is the governing domain evidence. The RAF-Alignment.xlsx text file was also searched for all three variant notations and contained no matching variant row.
Applicable only to critical and well-established functional domains available in the supplementary table (exon 6, exon 11, P-loop \[AA 459-474\], CR3 activation segment \[AA 594-627\]). Not applicable to specific amino acid residues (see PM5).
The VCEP's PP3 rule covers missense variants through the named REVEL predictor and requires REVEL ≥ 0.7. This variant is missense, NP_004324.2:p.(Leu597Arg), and the cited REVEL lookup reports 0.964, which meets the VCEP threshold. The SpliceAI result was not used for PP3 because the missense REVEL path independently satisfies the rule and the VCEP does not name SpliceAI as a required predictor for this situation.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
The governing BRAF VCEP applies PM2 at Supporting strength when the variant is absent from controls in gnomAD. The variant is absent from gnomAD v2.1, including the available non-cancer subset, but is present in the default all-comers gnomAD v4.1 dataset at AF 6.20073515916047e-07 (1/1,612,712 alleles; 0 homozygotes). Because the VCEP rule requires absence from gnomAD and the default all-comers gnomAD v4.1 record contains one allele, PM2 is not met.
The variant must be absent from controls (gnomAD).
The governing BRAF VCEP sets BA1 at a gnomAD filtering allele frequency of at least 0.05%. gnomAD v4.1 reports NM_004333.6:c.1790T>G at total AF 6.20073515916047e-07 (0.0000620074%), with 1 of 1,612,712 alleles and 0 homozygotes; the highest reported population AF is 8.482641969737327e-07 (0.0000848264%) in the European non-Finnish population. Both are below 0.05%, so BA1 is not met.
GnomAD filtering allele frequency ≥0.05%.
The governing BRAF VCEP sets BS1 at a gnomAD filtering allele frequency of at least 0.025%. gnomAD v4.1 reports NM_004333.6:c.1790T>G at total AF 6.20073515916047e-07 (0.0000620074%), and the highest reported population AF is 8.482641969737327e-07 (0.0000848264%) in the European non-Finnish population. Both are below 0.025%, so BS1 is not met.
GnomAD filtering allele frequency ≥0.025%.
The VCEP's BP4 rule applies to missense variants using the named REVEL predictor and requires REVEL ≤ 0.3. This variant is missense, but the cited REVEL lookup reports 0.964, which is above the VCEP benign threshold; therefore BP4 is not met. The SpliceAI result is not substituted for the governing missense REVEL rule.
For missense variants: REVEL ≤0.3.
The BRAF VCEP requires the same amino acid change as a previously established pathogenic variant. PMID:22798288 reports the exact BRAF c.1790T>G (p.L597R) somatic change and PMID:24933606 discusses BRAF L597R, but the extracted evidence does not establish a pathogenic germline comparator under the VCEP rule. The RAF-Alignment.xlsx text file was searched for c.1790T>G, p.Leu597Arg, and p.L597R with no entry found.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in _BRAF_ and _RAF1_.
PS2 cannot be assessed because the available case evidence does not document a proband with a RASopathy phenotype who has a confirmed de novo NM_004333.6:c.1790T>G variant, confirmation of both maternity and paternity, or absence of a family history. The VCEP assigns PS2 strength by de novo point evidence, but no PS2 points can be established from the available evidence.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. ... 4 Points. ... 2 Points. ... 1 Point.
The BRAF VCEP applies PS4 using point-based scoring for autosomal-dominant RASopathy cases, with full points for RASopathy phenotypes and reduced points for minimal phenotypic information. The available literature includes somatic melanoma and other cancer studies, but no verified germline RASopathy case series with affected-versus-control counts, a case-control OR/RR and 95% CI, or sufficient unrelated RASopathy proband observations to assign PS4 points. PMID:22798288 reports L597R in a metastatic melanoma tumor and explicitly provides no segregation or population-frequency data; PMID:26643848 groups L597 substitutions without L597R-specific case data; PMID:22142829 does not mention L597R. Therefore PS4 cannot be evaluated under the VCEP rule without substituting non-VCEP evidence.
Strength adjustment using point-based scoring for autosomal dominant cases with phenotypic specifications: full points awarded with RASopathy phenotypes, reduced points applicable to cases with minimal phenotypic information (i.e. prenatal cases, cases with a clinical order of a RASopathy panel without clinical information, and cases with limited clinical information in other global tests (such as WES)). ... The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. ... Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence.
The BRAF VCEP permits PM5 at Moderate strength when one likely pathogenic residue change at the same codon is documented. The available PM5 candidate collection contains zero same-residue candidates, and no matching entry for c.1790T>G, p.Leu597Arg, or p.L597R was found in RAF-Alignment.xlsx.txt. The literature extract for PMID:26643848 describes L597 substitutions but does not provide variant-specific pathogenic evidence for L597R.
1 \[likely\] pathogenic residue change at the same codon.
PM6 cannot be assessed because the available case evidence does not document an assumed de novo NM_004333.6:c.1790T>G observation, a RASopathy phenotype, parental testing, or a VCEP point assignment. The VCEP provides 2-point, 1-point, and 0.5-point PM6 levels, but no qualifying observation is available.
Assumed de novo, but without confirmation of paternity and maternity. ... 2 Points. ... 1 Point. ... 0.5 Points.
PP1 cannot be assessed because the available case evidence contains no affected relatives, family segregation results, or informative meioses for NM_004333.6:c.1790T>G. The VCEP requires at least 3 informative meioses for supporting strength, 5 for moderate, or 7 for strong strength.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... Segregation in more than one family is recommended. ... ≥7 informative meioses. ... ≥5 informative meioses. ... ≥3 informative meioses.
The VCEP requires a gnomAD missense z score greater than 3.09. The available case evidence does not provide a BRAF missense z score, so PP2 cannot be evaluated without substituting a generic metric or threshold.
Missense z score is >3.09 in gnomAD.
The governing BRAF VCEP evaluates BS2 through phenotype-based point scoring: -4 points for strong evidence or -1 point for supporting evidence, using healthy homozygote or heterozygote individuals and reduced points for apparently unaffected heterozygous individuals. gnomAD v4.1 reports 0 homozygotes, but the available population record does not establish healthy individual status, genotype-level phenotype, penetrance, age, or the VCEP's required point assignment. Therefore BS2 cannot be assessed from the available evidence.
\-4 Points. ... \-1 Point.
BS4 cannot be assessed because the available case evidence does not document affected relatives who lack NM_004333.6:c.1790T>G or any informative meiosis demonstrating non-segregation. The VCEP requires one informative meiosis, which is not available.
Lack of segregation in affected members of a family. ... Requires only one informative meiosis.
BP2 is applicable in the BRAF RASopathy VCEP framework, but the available evidence does not document an alternative molecular cause of a RASopathy in the same gene, a second pathogenic variant in cis or trans, parental/offspring testing, or a phenotype consistent with the required alternative-cause scenario. The VCEP's point threshold therefore cannot be evaluated.
Points are awarded for an alternative molecular cause of a RASopathy in the same gene (and/or in conjunction with BP5) and the phenotype is consistent with expected severity of the RASopathy. ... ≥ (-1) Point.
The BRAF VCEP BP5 rule requires an alternative molecular cause of a RASopathy in a different gene, or a phenotype inconsistent with RASopathy fully explained by a different causative variant, with point-based strength adjustment. The available case evidence identifies BRAF L597R in somatic cancer and provides no documented alternate germline causative variant, phenotype-inconsistent RASopathy assessment, or VCEP BP5 point assignment. BP5 therefore cannot be evaluated without substituting a generic or non-VCEP rule.
Points are awarded for an alternative molecular cause of a RASopathy in a different gene (and/or in conjunction with BP2) and the phenotype is consistent with expected severity of the RASopathy. Points are also awarded for phenotypes inconsistent with a RASopathy and fully explained by a different causative variant (e.g. WES testing). ... ≥ (-4) Points. ... ≥ (-2) Points. ... ≥ (-1) Point.
PVS1 is not applicable under the BRAF VCEP specification. The variant is NM_004333.6:c.1790T>G, a missense substitution producing p.(Leu597Arg) in exon 15, not a null variant of the types listed in the VCEP's PVS1 summary; the CSPEC entry explicitly marks PVS1 not applicable.
Not applicable.
PM3 is not applicable under the BRAF RASopathy VCEP specification. The VCEP explicitly marks PM3 as not applicable and gives no PM3 strength rule for this framework, regardless of the available phase or affected-proband evidence.
Not applicable.
PM4 is not applicable to this variant. The VCEP rule states "No known repetitive areas in gene. Use as described." The observed change is a single missense substitution, p.(Leu597Arg), with no protein-length change or in-frame insertion/deletion; therefore it is outside the PM4 consequence class being used here.
No known repetitive areas in gene. Use as described.
The BRAF VCEP explicitly marks PP4 as not applicable and directs phenotype-specific evidence to PS4.
Not applicable, see PS4.
The BRAF VCEP marks PP5 as not applicable for this VCEP and states that the criterion is not for use.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
BS3 is not applicable under the BRAF VCEP v2.3 CSPEC entry, which explicitly marks BS3 as Not applicable. The available functional evidence is also activating/damaging rather than evidence of no damaging effect: p.L597R increased phospho-MEK and phospho-ERK in the variant-specific cellular assay. The governing functional-studies table was searched for c.1790T>G, p.Leu597Arg, and p.L597R and contains no variant-specific entry or pre-assigned code for this variant.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The variant is a missense change, p.(Leu597Arg). The BRAF VCEP limits BP1 to truncating variants such as nonsense, frameshift, canonical splice-site, initiation-codon, whole-gene, or multi-exon deletions in genes without established loss-of-function correlation; this missense variant is outside those named variant types.
This rule has contraindications for use with RASopathies. Given the disease mechanism is gain-of-function for RASopathies, BP1 should be used for any truncating variant (nonsense, frameshift, affects canonical splice sites, initiation codon, entire gene or multi exon deletion) in genes without established LOF correlation to disease. See the supplemental material regarding dosage sensitivity information for each individual gene and potential association to disorders associated with LOF variants.
BP3 is not applicable under the BRAF VCEP specification. The CSPEC entry marks BP3 not applicable and states that there are no known benign repetitive areas in RASopathy genes; this variant is also a missense substitution rather than an in-frame deletion or insertion in a repetitive region without known function.
No known benign repetitive areas in RASopathy genes.
The BRAF VCEP marks BP6 as not applicable for this VCEP and states that the criterion is not for use.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The VCEP's BP7 rule is limited to synonymous variants, intronic positions except canonical splice sites, or non-coding variants. This variant is a missense substitution, NM_004333.6:c.1790T>G / NP_004324.2:p.(Leu597Arg), so it lies outside BP7's stated scope and BP7 is not applicable before evaluating splice-prediction or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
Every interpreted variant in BRAF, mapped onto the exon structure of NM_004333.6. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)1 / 1,178,878 | 8.5e-07 |
This variant is present in gnomAD v4.1 (AF= 6.20074e-07; MAF= 0.00006%, 1/1612712 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.48264e-07; MAF= 0.00008%, 1/1178878 alleles, homozygotes = 0).
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
The VCEP's PP3 rule covers missense variants through the named REVEL predictor and requires REVEL ≥ 0.7. This variant is missense, NP_004324.2:p.(Leu597Arg), and the cited REVEL lookup reports 0.964, which meets the VCEP threshold. The SpliceAI result was not used for PP3 because the missense REVEL path independently satisfies the rule and the VCEP does not name SpliceAI as a required predictor for this situation.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
The VCEP's BP4 rule applies to missense variants using the named REVEL predictor and requires REVEL ≤ 0.3. This variant is missense, but the cited REVEL lookup reports 0.964, which is above the VCEP benign threshold; therefore BP4 is not met. The SpliceAI result is not substituted for the governing missense REVEL rule.
For missense variants: REVEL ≤0.3.
The VCEP's BP7 rule is limited to synonymous variants, intronic positions except canonical splice sites, or non-coding variants. This variant is a missense substitution, NM_004333.6:c.1790T>G / NP_004324.2:p.(Leu597Arg), so it lies outside BP7's stated scope and BP7 is not applicable before evaluating splice-prediction or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
SpliceAI predicts possible splice impact for this variant (max delta score = 0.49). REVEL score = 0.964. BayesDel score = 0.468901.
8 paper records listed. 2 cited in the classification.
The validated somatic SNP with the combined highest depth of coverage (DP) and quality (qual) scores was BRAF L597R (c.1790T>G) (Fig. 1, Supplementary Fig. S7, and Supplementary Table S8).
Location Results, Identification of a BRAF L597R mutation by whole genome sequencing; Results, Signaling induced by BRAF L597 and K601E mutants is suppressed by a MEK inhibitor
Context Whole-genome sequencing and validation in a tumor/normal pair from metastatic melanoma, followed by ectopic-expression and drug-treatment assays in 293H cells measuring phospho-MEK and phospho-ERK.
An in-vitro study of patient-derived tumour material harbouring an L597R mutation showed ERK activation to be abrogated with BRAF inhibitors: vemurafenib, dabrafenib and the multikinase inhibitor sorafenib. This patient showed a partial response to vemurafenib treatment [11].
Location Introduction, paragraph discussing activating BRAF K601E and L597 mutations
Context In-vitro analysis of patient-derived tumor material harboring BRAF L597R, assessing ERK activation after exposure to vemurafenib, dabrafenib, and sorafenib.
The L597 mutations result in an amino acid substitution at position 597 in BRAF, from a leucine (L) to a serine (S), glutamine (Q) or arginine (R). Mutations at both codons result in elevated kinase activity similar to mutations at V600
Introduction, paragraph describing codons L597 and K601
BRAF mutations were identified in 1% (2/192) of NB samples, 1.7% (1/60) of ERMS samples, and 1.3% (1/75) of ES samples. The ERMS and ES samples harbored the activating BRAFV600E mutation. One NB sample carried the BRAFV600E mutation, while the other carried the less common BRAFD594V mutation.
Results, paragraph 4
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The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 6.20074e-07; MAF= 0.00006%, 1/1612712 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.48264e-07; MAF= 0.00008%, 1/1178878 alleles, homozygotes = 0).
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 13968)
SpliceAI predicts possible splice impact for this variant (max delta score = 0.49). REVEL score = 0.964. BayesDel score = 0.468901.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56121113, n = 37 times).
This variant lies in a statistically significant hotspot.