The BRAF NM_004333.6:c.1798_1799delinsAA (NP_004324.2:p.(Val600Lys)) missense variant has previously been reported in somatic cancers (COSMIC; COSV56057713, n = 764 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: BRAF V600K activated both MEK and ERK, satisfying the VCEP rule that two different approved assays support Moderate PS3. 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 at Moderate: BRAF V600K activated both MEK and ERK, satisfying the VCEP rule that two different approved assays support Moderate PS3.
Met, Moderate: residue 600 falls within the VCEP-approved CR3 activation segment domain spanning amino acids 594-627.
Met, supporting: the variant is absent from both default all-comers gnomAD v2.1 and v4.1 control datasets.
No benign criterion marked as applied in the recorded assessment.
VUS: PS3 (moderate), PM1 (moderate), and PM2 (supporting) do not satisfy any 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 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.057. Refer to the recorded PP3/BP4 rationale for interpretation.
1 Uncertain significance. ClinVar API review status: no assertion criteria provided.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV56057713, n = 764 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 · 3 not met · 13 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Functional evidence supports PS3 at Moderate strength because PMID:26343582 reports abnormal MEK and ERK activation for BRAF V600K, representing two different approved VCEP assay types; BS3 is not applicable under the BRAF VCEP specification.
PS4 is not assessed because the VCEP-required phenotype point total and case-control or sufficient unrelated-case data are unavailable.
PP4, PP5, and BP6 are not applicable under the BRAF VCEP specification.
BP5 is not assessed because no alternative molecular cause or VCEP point assignment is documented.
No criteria match.
PS3 is met at Moderate strength. PMID:26343582 explicitly studied BRAF V600K, corresponding to NM_004333.6:c.1798_1799delinsAA and NP_004324.2:p.(Val600Lys), in inducible NIH3T3-cell assays. The study reported significant induction of phosphorylated MEK and phosphorylated ERK, demonstrating abnormal activation of the RAS/MAPK pathway. The VCEP approved-functional-studies file identifies MEK Activation Assay and ERK Activation Assay as approved pathway-specific assay types for BRAF, each with PS3_Supporting proposed strength, and states that two or more unique assay types for a variant support upgrading PS3 to Moderate. The variant was not listed as a pre-assigned row in SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx under c.1798_1799delinsAA, p.Val600Lys, or p.V600K; therefore the Moderate assignment is based on the VCEP's approved assay-type rule and the variant-specific paper evidence rather than a table-specific pre-assigned variant code.
Two or more different approved assays.
The VCEP limits PM1 at Moderate strength to critical and well-established functional domains listed in its supplementary table: exon 6, exon 11, P-loop residues 459-474, and the CR3 activation segment residues 594-627. The variant is p.Val600Lys/p.V600K, placing residue 600 within the explicitly approved CR3 activation segment. vcep_materials.json has no domain_tables entry for BRAF, so the governing CSPEC domain specification is the available authoritative domain list. RAF-Alignment.xlsx.txt was also searched as the declared PM1 file, but it contains no V600K or residue-600 BRAF entry; this does not remove the direct CSPEC domain match.
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 governing BRAF VCEP assigns PM2 at supporting strength when the variant is absent from controls in gnomAD. The variant is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, satisfying the VCEP rule.
The variant must be absent from controls (gnomAD).
PM4 applies to protein length changes caused by in-frame deletions/insertions in a non-repeat region or to stop-loss variants. This variant is a two-nucleotide delins that produces the missense substitution p.(Val600Lys), with no protein length change and no stop-loss consequence; therefore PM4 is not met. The VCEP states that BRAF has no known repetitive areas, but that does not convert a missense substitution into a qualifying protein-length change.
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. ... No known repetitive areas in gene. Use as described.
The governing BRAF VCEP applies BA1 at stand-alone strength when the gnomAD filtering allele frequency is at least 0.05%. This variant is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, so no qualifying filtering allele frequency is present and BA1 is not met.
GnomAD filtering allele frequency ≥0.05%.
The governing BRAF VCEP applies BS1 at strong strength when the gnomAD filtering allele frequency is at least 0.025%. This variant is absent from the default all-comers gnomAD v2.1 and v4.1 datasets, so no qualifying filtering allele frequency is present and BS1 is not met.
GnomAD filtering allele frequency ≥0.025%.
The BRAF VCEP rule requires the same amino-acid change as a previously established pathogenic variant and permits the criterion for analogous BRAF and RAF1 residue positions. The case evidence identifies the variant as p.Val600Lys (p.V600K), but ClinVar reports it as uncertain significance without expert-panel criteria, and the consulted literature extraction reports V600K functional studies without establishing a previously established pathogenic variant. The required pathogenic comparator is therefore not demonstrated by the available VCEP-governed evidence.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in _BRAF_ and _RAF1_.
The VCEP evaluates PS2 using point-based de novo evidence in conjunction with PM6 and phenotype specifications. The available case evidence does not document a proband with a RASopathy phenotype, confirmed maternity and paternity, absence of family history, or any parental testing result; therefore no PS2 points or strength can be assigned.
Follow SVI recommendations for point-based scoring in conjunction with PM6 (see Reference 1) and 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 BRAF VCEP applies PS4 using phenotype-specific point scoring for autosomal-dominant RASopathy cases. The available literature packet has no ai_classified_papers, and the variant-specific full-text paper reviewed (PMID:26343582) is a cellular signaling study, not a case-control study and does not provide affected-case/control counts, an odds ratio, a confidence interval, or a VCEP PS4 point assignment. The case evidence also provides no unrelated affected-patient count or matched control comparison from which to compute an odds ratio. Therefore the VCEP PS4 point total cannot be evaluated; no PS4 strength is assigned.
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 VCEP PM5 rule requires one likely pathogenic residue change at the same codon for Moderate strength, or at least two different likely pathogenic residue changes at the same codon observed in at least five probands for Strong strength. The collected PM5 candidate record contains zero same-residue candidates and no expert-panel or non-expert majority likely-pathogenic comparators. No qualifying same-codon comparator is therefore available to apply either strength.
1 \[likely\] pathogenic residue change at the same codon.
The VCEP assigns PM6 strength by point-based scoring for an assumed de novo variant, with full or reduced points determined by phenotype information. The available evidence contains no parental testing, maternity or paternity information, de novo observation, or usable phenotype description; the 2-point, 1-point, and 0.5-point PM6 paths therefore cannot be evaluated.
Follow SVI recommendations for point-based scoring in conjunction with PS2 (see Reference 1) and 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 VCEP applies PP1 to informative meioses, with Supporting, Moderate, and Strong evidence requiring at least 3, 5, and 7 informative meioses, respectively; it also recommends segregation in more than one family. No affected relatives, familial genotypes, informative meioses, or segregation observations are documented, so PP1 cannot be assessed.
Segregation in more than one family is recommended.
The VCEP PP2 rule requires a missense z score greater than 3.09 in gnomAD. The available case evidence contains no BRAF missense z score; the gnomAD records provide variant absence but not the required gene-level missense z score. The criterion cannot be evaluated under the VCEP rule.
Missense z score is >3.09 in gnomAD.
The variant is a missense change, p.(Val600Lys), so the applicable VCEP computational path is the missense path requiring REVEL >=0.7. No REVEL score is available. The VCEP also states that, for a splicing-impact path, the predicted outcome must match the disease mechanism, but it does not name SpliceAI or provide a splice-prediction cutoff; therefore the available SpliceAI result (maximum delta score 0.057) is not substituted for the named missense predictor and PP3 cannot be assessed.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
The governing BRAF VCEP expresses BS2 as a point-based rule, with strong evidence at -4 points and supporting evidence at -1 point. The available case evidence contains population absence results but no qualifying healthy-individual, homozygote, or point-assignment data; therefore BS2 cannot be evaluated.
Strong: -4 Points. Supporting: -1 Point.
The VCEP defines BS4 as lack of segregation in affected family members and permits Strong evidence with one informative meiosis. The available evidence documents no affected family members, familial variant testing, non-segregation observation, or informative meiosis; BS4 cannot therefore be assessed.
Lack of segregation in affected members of a family.
BP2 is applicable under the VCEP, but it requires point assignment for an alternative molecular cause of a RASopathy in the same gene, with phenotype consistent with the expected severity, and the available case evidence provides no documented second pathogenic BRAF variant, phase result, cis/trans relationship, affected-proband observation, or phenotype-based point assignment. The VCEP's supporting threshold is at least -1 point, but the required points cannot be determined from the available evidence; BP2 is therefore not assessed rather than inferred absent.
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 variant is a missense change, p.(Val600Lys), and therefore lies within the VCEP BP4 missense scope. The governing rule requires REVEL <=0.3. No REVEL score is available; the available SpliceAI score is not the predictor named for this missense BP4 path and cannot replace REVEL.
For missense variants: REVEL ≤0.3.
The BRAF VCEP allows BP5 when an alternative molecular cause of RASopathy is present in a different gene, or when an inconsistent phenotype is fully explained by a different causative variant, with points awarded according to the VCEP's phenotypic specifications. The available case evidence identifies no alternative causative variant, no different-gene molecular diagnosis, and no phenotype-specific BP5 point total. Therefore BP5 cannot be evaluated under the 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).
PVS1 is not applicable under the BRAF VCEP specification. The variant is NM_004333.6:c.1798_1799delinsAA, a missense variant producing NP_004324.2:p.(Val600Lys) in exon 15, rather than a null variant of the types named by the governing PVS1 description; no PVS1 strength is assigned.
Not applicable. ... Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
PM3 is not applicable under the ClinGen RASopathy Expert Panel BRAF Version 2.3 specification. The VCEP explicitly marks PM3 as not applicable, so no recessive-disorder phase or trans-observation assessment is performed for this autosomal-dominant RASopathy framework.
Not applicable.
The BRAF VCEP explicitly marks PP4 as not applicable and directs phenotype-specific evidence to PS4 instead. PP4 is not independently evaluated.
Not applicable, see PS4.
The BRAF VCEP marks PP5 not applicable for this VCEP and states that the criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Literature classifications therefore cannot establish PP5 under this governing framework.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
BS3 is not applicable under the ClinGen RASopathy Expert Panel BRAF Version 2.3 specification. The CSPEC entry explicitly marks BS3 as not applicable, so normal functional results cannot be used to assign BS3 under this VCEP framework. The approved-functional-studies table likewise lists BS3_NA for the BRAF MEK Activation Assay and ERK Activation Assay entries. No entry for c.1798_1799delinsAA, p.Val600Lys, or p.V600K was found in SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx.
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.Val600Lys/p.V600K. The BRAF VCEP BP1 rule is restricted to truncating variants, specifically nonsense, frameshift, canonical splice-site, initiation-codon, entire-gene, or multi-exon deletions, in genes without established loss-of-function correlation. This missense variant is outside the variant types named by the rule.
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 explicitly not applicable in the ClinGen BRAF VCEP specification. Although the VCEP describes the general ACMG/AMP BP3 concept as an in-frame deletion or insertion in a repetitive region without a known function, this BRAF VCEP does not permit BP3 for RASopathy genes.
No known benign repetitive areas in RASopathy genes.
The BRAF VCEP marks BP6 not applicable for this VCEP and states that the criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Benign literature reports therefore cannot establish BP6 under this governing framework.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The variant is a missense change, p.(Val600Lys), not a synonymous variant, an intronic variant outside a canonical splice site, or a non-coding variant. It is therefore outside the VCEP-defined BP7 scope, regardless of the available splice-prediction result.
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 |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
The variant is a missense change, p.(Val600Lys), so the applicable VCEP computational path is the missense path requiring REVEL >=0.7. No REVEL score is available. The VCEP also states that, for a splicing-impact path, the predicted outcome must match the disease mechanism, but it does not name SpliceAI or provide a splice-prediction cutoff; therefore the available SpliceAI result (maximum delta score 0.057) is not substituted for the named missense predictor and PP3 cannot be assessed.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
The variant is a missense change, p.(Val600Lys), and therefore lies within the VCEP BP4 missense scope. The governing rule requires REVEL <=0.3. No REVEL score is available; the available SpliceAI score is not the predictor named for this missense BP4 path and cannot replace REVEL.
For missense variants: REVEL ≤0.3.
The variant is a missense change, p.(Val600Lys), not a synonymous variant, an intronic variant outside a canonical splice site, or a non-coding variant. It is therefore outside the VCEP-defined BP7 scope, regardless of the available splice-prediction result.
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 no significant splice impact for this variant (max delta score = 0.06).
7 paper records listed. 1 cited in the classification.
Inductions of the expression of BRAF V600E, V600K, K601E, L597Q, G469A, G469V, or G464V at levels comparable to those of endogenous BRAF caused significant induction of p-MEK and p-ERK and marked inhibition of RAS-GTP and pCRAF S338.
Location Results, ‘Activating mutants of BRAF hyperactivate ERK signaling and suppress RAS activation’
Context Inducible BRAF expression in NIH3T3 cells; RAS-dependence assessed in lapatinib-treated SKBR3 cells and conditional RAS-less mouse embryo fibroblasts.
As expected, the V600E, G469A, T599_V600insT and V600_K601delinsE mutations all demonstrated increased BRAF kinase activity compared with wild type (WT) BRAF (Fig 1A). The increased kinase activity was associated with an increase in pERK 1/2 (Fig. 1B) and transformation in a soft agar assay (Fig. 1C).
Results, “Biological and clinical significance of selected non-V600E BRAF mutations,” paragraph 1
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The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 375941)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56057713, n = 764 times).
This variant lies in a statistically significant hotspot.