No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.
Likely pathogenic.A likely pathogenic classification under the recorded framework.
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 strength: two or more VCEP-approved functional assays show V600E increases MEK/ERK pathway signaling.
Met at moderate strength: residue 600 lies within the VCEP-approved CR3 activation segment (amino acids 594-627).
Met at supporting strength: the variant is effectively absent from gnomAD, with 2 of 1,612,922 v4.1 exome alleles (AF 1.24e-06). Strictly read, 1-2 observed alleles do not satisfy 'absent', and supporting is the only tier this ruleset allows.
Met at supporting strength: REVEL 0.931 exceeds the VCEP missense threshold of 0.7.
No benign criterion marked as applied in the recorded assessment.
Likely Pathogenic from 2 moderate criteria (PS3, PM1) plus 2 supporting criteria (PM2, PP3) under BRAF v2.3 Rule14.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 2 / 1,612,922 alleles. Recorded AF 1.23999e-06. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.97994e-06; MAF= 0.00040%, 1/251260 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.931. Refer to the recorded PP3/BP4 rationale for interpretation.
7 Pathogenic · 2 Likely pathogenic · 2 Uncertain significance.
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; COSV56056643, n = 31792 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: 4 met · 7 not met · 9 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Framework: the governing specification is the ClinGen RASopathy Expert Panel specification for BRAF v2.3 (cspec doc 643243119, framework_mode=vcep, precedence rank 1); all five criteria in this group were adjudicated against that VCEP text, with generic ACMG/AMP used only where the VCEP is silent.
Variant/codon context: NM_004333.6:c.1799T>A = NP_004324.2:p.(Val600Glu), missense, exon 15, codon 600 (GTG>GAG); the variant is essentially absent from gnomAD, so residue 600 carries no benign population variation.
PM1 met at Moderate: residue 600 lies within the VCEP-approved CR3 activation segment (AA 594-627), one of the four critical well-established functional domains the VCEP permits for PM1 (exon 6, exon 11, P-loop AA 459-474, CR3 AA 594-627); the VCEP rule is domain-based and forbids residue-specific reasoning under PM1, and the VCEP domain_tables object is empty so the rule text itself supplied the domain list.
PS1 not applicable to this variant: the only retrieved p.(Val600Glu) record is the identical c.1799T>A change, so no distinct alternate-nucleotide same-amino-acid comparator exists in evidence, and the BRAF/RAF1 analogous-residue branch could not be checked because the VCEP RAF alignment is image-only.
PM5 not assessed: the dedicated same-codon comparator search returned zero usable candidates and no other bundle source documents individually citable pathogenic codon-600 substitutions, so PM5 would require an ungrounded comparator claim.
PP2 not assessed: the VCEP rule requires a BRAF gnomAD missense z score >3.09 and no gene-level constraint value exists anywhere in this case's evidence.
BP1 not applicable: the VCEP confines BP1 to truncating variants under the gain-of-function RASopathy mechanism, and this is a missense substitution.
Framework used: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119; RASopathy, autosomal dominant; rule_payload gives a criteria-combination scoring model). All four criteria assigned to this group (PS2, PM6, PP1, BS4) are flagged Applicable in that specification, so generic ACMG/AMP definitions were used only to read the underlying criterion intent, with the VCEP strength/point thresholds applied where applicable.
VCEP strengths relevant here: PS2 and PM6 use the SVI de novo point system (PS2: 1/2/4 points = Moderate/Strong/Very Strong; PM6: 0.5/1/2 points = Supporting/Moderate/Strong) with full points only for RASopathy phenotypes and reduced points when phenotypic information is minimal; PP1 uses >=3/>=5/>=7 informative meioses = Supporting/Moderate/Strong with segregation in more than one family recommended; BS4 is Benign Strong and requires only one informative meiosis.
This case is a variant-level review of BRAF NM_004333.6:c.1799T>A (p.Val600Glu) with no proband, no phenotype, no family history, no parental testing and no segregation data. Consequently none of PS2, PM6, PP1 or BS4 can be assessed: there is no de novo or assumed de novo occurrence to score and no informative meiosis in either direction.
No pathogenic or benign weight is contributed by this group. Any final classification must therefore rest on the other criterion groups; PS2/PM6/PP1 were not affirmed, and BS4 was neither met nor excluded.
Framework-specific context worth recording: this residue change is the predominant recurrent somatic BRAF mutation in cancer (PMID:12068308), so de novo status can only be credited from germline (non-tumour) testing with confirmed maternity and paternity.
Governing framework: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119), applied because the case was run in vcep mode for BRAF; generic ACMG/AMP rules were not used to score any criterion in this group.
No criterion in this group is met. PS4 and BP5 could not be scored because the framework requires case-level, phenotype-specified point scoring and the bundle contains no case-level clinical, phenotype, or point data (both not_assessed). PP4 is not applicable under the VCEP, which routes phenotype specificity into PS4. PP5 and BP6 were assessed against the exact-variant ClinVar expert-panel gate and are not met: the record has 0 expert-panel submissions and single-submitter review status, so its aggregate laboratory labels cannot trigger either criterion.
The exact-variant evidence that does exist is dominated by somatic tumour observations (COSMIC somatic count 31,792; melanoma, papillary thyroid carcinoma, colorectal carcinoma, low-grade astrocytoma, germ cell tumour, vascular malformation) and by functional GOF assays; neither supplies germline case-control enrichment or phenotype specificity for a RASopathy proband, and genomic/functional criteria are adjudicated by other groups.
Governing framework: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3 (CSPEC doc 643243119) is present and applicable, so the generic lab fallback thresholds for PP3/BP4 (generic REVEL 0.750/0.250 cutoffs, generic SpliceAI 0.2/0.1 cutoffs) were not used.
Variant consequence type is missense: NM_004333.6:c.1799T>A -> NP_004324.2:p.(Val600Glu) (BRAF V600E, exon 15 kinase domain). Exactly one computational path - the missense protein-impact path - was therefore evaluated, per the VCEP rule 'For missense variants: REVEL >= 0.7'.
PP3 met (supporting): local REVEL v1.3 score 0.931 >= 0.7 BRAF VCEP cutoff.
BP4 not met: the BRAF VCEP BP4 missense rule requires REVEL <= 0.3; observed REVEL is 0.931.
BP7 not applicable: the variant is a missense, not a synonymous/intronic (non-canonical)/non-coding variant, which is BP7's precondition.
No double counting: the REVEL score was used only once (PP3); SpliceAI (max delta 0.007, no predicted splice impact) was recorded as checked but was not used as support for the missense variant's PP3/BP4, and absence of predicted splice impact is not evidence about the substituted amino acid.
BayesDel (0.335473) was not used for PP3/BP4 because no verified published BayesDel threshold is available to this pipeline.
No BRAF VCEP PP3/BP4 lookup spreadsheet pre-assigning a code for this variant was found; the VCEP materials present (RAF-Alignment.xlsx for analogous-residue analyses; SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx for functional assays) contain no in-silico per-variant assignments.
All four population criteria were adjudicated against the governing ClinGen RASopathy Expert Panel BRAF specification v2.3 (cspec), which supplies the applicable thresholds: BA1 = gnomAD filtering allele frequency >=0.05% (stand alone); BS1 = gnomAD filtering allele frequency >=0.025% (strong); PM2 = absent from controls (gnomAD), Supporting tier only; BS2 = point-based (-4 Strong / -1 Supporting) using healthy homozygous or healthy heterozygous individuals, including apparently unaffected heterozygous parent/sibling samples. Generic ACMG/AMP frequency thresholds were not needed because a gene-specific specification exists.
Population frequency is essentially null: 1/251,260 exome alleles in gnomAD v2.1 (AF 3.98e-06, homozygotes = 0) and 2/1,612,922 exome alleles in gnomAD v4.1 (AF 1.24e-06, homozygotes = 0), with the single South Asian observation being the only non-zero ancestry group and no homozygote anywhere.
Benign frequency criteria therefore fail by a wide margin: the highest observed subpopulation AF (3.267e-05 in v2.1; 1.098e-05 in v4.1) is still ~8-23 fold below the BS1 0.025% threshold and ~15-45 fold below the BA1 0.05% threshold, so no benign stand-alone or benign strong population evidence is available for this variant.
BS2 fails because its required observations are absent rather than merely weakly documented: zero homozygotes in both datasets, no phenotyped healthy heterozygous adult, and no genotype/phenotype data for unaffected parents or siblings in the bundle; RASopathy is an autosomal dominant condition with age-dependent, incomplete penetrance, so unscreened heterozygous presence in a population database cannot demonstrate a healthy adult in whom full penetrance at an early age would be expected.
PM2 is met at the CSPEC-permitted Supporting strength: the variant is present at a rate (1-2 alleles in >1.6 million) that is ~3-4 orders of magnitude below the cohort-level thresholds of the same specification, with no homozygotes and no ancestry-specific enrichment. The only interpretive tension is the literal CSPEC wording 'must be absent' versus 1-2 observed alleles; this is flagged in the PM2 gaps_remaining and in the group warnings, and the frequency evidence is recorded as quantitative rather than absolute.
Threshold/artefact considerations were explicitly checked: (a) gnomAD grpmax filtering allele frequency — the statistic named by the BA1/BS1 rules — was not returned by the lookup (null for v2.1 and v4.1), so popmax subpopulation AF was used as a conservative upper bound and the benign criteria still fail; (b) the gnomAD genome component contributed no alleles in either dataset (genome_an = 0), so all frequencies are exome-only; (c) gnomAD-Canada v1.0 (HostSeq) timed out, leaving the Canadian cohort unchecked; (d) because this variant is a dominant somatic hotspot (COSMIC COSV56056643, 31,792 somatic occurrences), low-level population observations may include somatic/mosaic or technical signal, which affects how 'absent' is interpreted for PM2 but cannot manufacture benign frequency evidence for BA1/BS1.
Group net effect on classification: PM2 Supporting (met) is the only population criterion satisfied; BA1, BS1 and BS2 are not met. Population data neither support a benign classification nor contradict a pathogenic one, and no benign stand-alone criterion was triggered.
No criteria match.
The BRAF VCEP Version 2.3 framework specifies PS3 Supporting for one approved assay and PS3 Moderate for two or more different approved assays. Variant-specific studies of BRAF V600E provide two biologically relevant, pathway-based functional readouts: elevated MEK phosphorylation/RAF-MEK pathway activity and increased ERK-dependent transcriptional output in V600E BRAF tumor cells, plus cell-based MEK/ERK signaling response to RAF inhibition. These correspond to distinct approved pathway functional assay types in the VCEP functional-studies resource and support the gain-of-function mechanism for BRAF V600E. No evidence supports escalation to Strong under the VCEP rule.
BRAF VCEP Version 2.3 PS3: Moderate = two or more different approved assays; Supporting = one approved assay.
The BRAF VCEP v2.3 restricts PM1 to critical, well-established functional domains named in its supplementary domain table: exon 6, exon 11, the P-loop (AA 459-474) and the CR3 activation segment (AA 594-627), and explicitly excludes residue-specific reasoning from PM1 (that is PM5's scope). p.(Val600Glu) alters residue 600, which falls inside the CR3 activation segment (AA 594-627) and is encoded by exon 15; membership in any single approved domain satisfies the rule. vcep_materials.json 'domain_tables' is empty for BRAF, so the authoritative approved-domain list was taken directly from the governing VCEP rule text rather than re-derived, and the VCEP RAF-Alignment workbook could not be parsed further (alignment sheet is image-only). PM1 is therefore met at Moderate strength on domain membership alone; the case hotspot artifact (statistically significant V600 hotspot, screenshot-level) and the domain-localising literature are corroborative only.
Moderate: 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).
BRAF RASopathy CSPEC v2.3 PM2 is 'The variant must be absent from controls (gnomAD)'; although the CSPEC default strength is listed as Pathogenic Moderate, only the Supporting tier is applicable in this ruleset, so PM2 can only be applied at Supporting. The variant is effectively absent: gnomAD v4.1 exomes contain 2/1,612,922 alleles (AF 1.24e-06; 0 homozygotes; popmax South Asian 1/91,076, AF 1.098e-05) and gnomAD v2.1 exomes contain 1/251,260 alleles (AF 3.98e-06; 0 homozygotes; popmax South Asian 1/30,612, AF 3.267e-05). Strictly read, 'absent' is not satisfied because 1-2 alleles were observed, so this call rests on the standard interpretation of the rule as 'absent or at extremely low frequency': the observation rate is ~3-4 orders of magnitude below the cohort-level thresholds used by this same specification (BS1 0.025%), is at the boundary of what allele-count-based databases can distinguish from a low-level somatic, mosaic, or technical signal for a variant that is a dominant somatic hotspot, and no homozygote or recurrent population haplotype is present. PM2 is therefore awarded at Supporting only, and its point value is small relative to the rest of the case. Human review is flag-free only because the frequency question itself is unambiguous; the interpretive caveat is recorded in gaps_remaining and warnings.
The variant must be absent from controls (gnomAD) — CSPEC BRAF v2.3, applicable strength tier: Supporting only.
NM_004333.6:c.1799T>A is a missense substitution, NP_004324.2:p.(Val600Glu) (BRAF V600E), so it is adjudicated on the missense protein-impact path. The governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) states for PP3: 'For missense variants: REVEL >= 0.7', at Pathogenic Supporting strength. The local REVEL v1.3 lookup returns REVEL = 0.931 for this variant, which exceeds the 0.7 VCEP cutoff, so PP3 is met at supporting strength. BayesDel (0.335473) was not used because no verified published calibration for these criteria is available to this pipeline. The SpliceAI result was deliberately NOT used as support: a spliced-path score cannot clear a missense variant's protein-level effect, and no predicted splice impact is not evidence about the substituted amino acid.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC PP3: for missense variants, REVEL >= 0.7 -> PP3 supporting
The variant is a missense substitution, p.(Val600Glu), with no protein-length change. It is neither an in-frame insertion/deletion nor a stop-loss variant, so PM4 is not met. The governing BRAF specification states that there are no known repetitive areas in the gene and otherwise uses PM4 as described.
ClinGen RASopathy Expert Panel BRAF v2.3: PM4 moderate; no known repetitive areas in BRAF; use as described.
PP5 is only triggered by an exact-variant ClinVar expert-panel (three-star) classification of Pathogenic or Likely pathogenic. For this variant the ClinVar record has 0 expert-panel submissions, the overall review status is 'criteria provided, single submitter', and every audited submission carries is_expert_panel = false; the assertions are ordinary laboratory/research submissions and the aggregate label, which must never trigger PP5. The exact-variant record is in fact Pathogenic overall, but that is an aggregate/non-expert label and is not usable evidence for PP5. Independently, the governing BRAF RASopathy VCEP v2.3 also marks PP5 as not for use ('not for use as recommended by the ClinGen SVI VCEP Review Committee'). PP5 is therefore not met.
PP5 requires an exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic assertion (three-star); ordinary laboratory submissions, aggregate labels and non-expert assertions never trigger it. ClinGen RASopathy Expert Panel BRAF v2.3 additionally designates PP5 as Not Applicable for this VCEP.
Governing framework is the ClinGen RASopathy Expert Panel BRAF specification v2.3 (cspec), which sets BA1 as stand-alone benign at a gnomAD filtering allele frequency >=0.05%. The variant is orders of magnitude below that: gnomAD v4.1 exomes show 2/1,612,922 alleles (AF 1.24e-06; 0 homozygotes) and gnomAD v2.1 exomes show 1/251,260 alleles (AF 3.98e-06; 0 homozygotes). Even taking the highest single-subpopulation frequency observed anywhere (South Asian, 3.267e-05 in v2.1; 1.098e-05 in v4.1) as a deliberately conservative upper bound for the CSPEC-specified filtering allele frequency, BA1 still fails by roughly 15-45 fold. No benign stand-alone population evidence exists, and no ancestry-specific or threshold artifact is large enough to change this. The generic ACMG/AMP fallback (>1-5% population frequency) is met even less.
GnomAD filtering allele frequency >=0.05% (Benign Stand Alone; only applicable tier in BRAF CSPEC v2.3).
BRAF RASopathy CSPEC v2.3 sets BS1 as benign strong at a gnomAD filtering allele frequency >=0.025%. Observed frequencies are far below that: gnomAD v4.1 exome total AF 1.24e-06 (2/1,612,922; 0 homozygotes) and gnomAD v2.1 exome total AF 3.98e-06 (1/251,260; 0 homozygotes). The highest any-subpopulation frequency (South Asian, 3.267e-05 in v2.1; 1.098e-05 in v4.1) — used as a deliberately conservative stand-in for the CSPEC-specified filtering allele frequency, which the lookup did not return — is still ~8-23 fold below the 0.025% threshold. The variant is therefore far rarer than expected for the RASopathy disease spectrum at the CSPEC-specified AF, and the standard ACMG/AMP reading of BS1 (allele frequency greater than expected for the disorder) is likewise unmet. No frequency-based benign strong evidence is available.
GnomAD filtering allele frequency >=0.025% (Benign Strong; only applicable tier in BRAF CSPEC v2.3).
BRAF RASopathy CSPEC v2.3 makes BS2 a point-based rule (-4 points = Strong; -1 point = Supporting) with explicit phenotypic specifications: points are based on healthy homozygous or healthy heterozygous individuals, with reduced points for apparently unaffected heterozygous individuals and applicability to parent or sibling samples during clinical family evaluations. None of the required observations exists for this variant. There are zero homozygotes in both population datasets examined (0/251,260 in gnomAD v2.1; 0/1,612,922 in gnomAD v4.1), so the Strong tier cannot be scored. The only observations are 1-2 heterozygous alleles in unscreened population samples, which carry no phenotype information; RASopathy (MONDO:0021060) is an autosomal dominant disorder with age-dependent, incomplete penetrance and variable expressivity, so mere presence of a heterozygous allele in a population database cannot establish an apparently healthy adult in whom full penetrance would be expected at an early age, nor an apparently unaffected heterozygous parent or sibling. The case bundle contains no genotype data for unaffected relatives of the proband. No BS2 points are therefore awarded.
Point-based BS2: >= -4 Points (Benign Strong) or >= -1 Point (Benign Supporting); phenotypic specifications require healthy homozygous/heterozygous individuals, with reduced points for apparently unaffected heterozygous individuals in parent or sibling samples (BRAF CSPEC v2.3).
NM_004333.6:c.1799T>A (p.Val600Glu) is a missense variant, so BP4 is assessed on the missense path. The governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) BP4 rule is 'For missense variants: REVEL <= 0.3'. The local REVEL v1.3 score is 0.931, which is far above 0.3, so the BP4 benign-supporting threshold is not met. The splice sub-rule of BP4 ('predicted outcome is negligible or does not match disease mechanism') cannot be used to meet BP4 for this missense variant, and in any case the CSPEC requires its in-silico criteria to be counted only once per variant; the same REVEL score that supports PP3 cannot also support BP4. BP4 is therefore not met.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC BP4: for missense variants, REVEL <= 0.3 -> BP4 supporting (not satisfied)
BP6 is only triggered by an exact-variant ClinVar expert-panel (three-star) classification of Benign or Likely benign. The ClinVar record for this variant has 0 expert-panel submissions and review status 'criteria provided, single submitter'; no expert-panel benign assertion exists, and the record's non-expert submissions are Pathogenic/Likely pathogenic/Uncertain significance only. Ordinary laboratory submissions, aggregate labels, and non-expert assertions must never trigger BP6, so the criterion is not met. Independently, the governing BRAF RASopathy VCEP v2.3 marks BP6 as not for use.
BP6 requires an exact-variant ClinVar expert-panel Benign/Likely benign assertion (three-star); ordinary laboratory submissions, aggregate labels and non-expert assertions never trigger it. ClinGen RASopathy Expert Panel BRAF v2.3 additionally designates BP6 as Not Applicable for this VCEP.
The applicable framework is the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119, RASopathy, autosomal dominant), in which PS2 is Applicable and scored with the SVI de novo point system (1 point = Moderate, 2 points = Strong, 4 points = Very Strong; full points with RASopathy phenotypes, reduced points when phenotypic information is minimal). PS2 requires a de novo occurrence with both maternity and paternity confirmed in a patient with the disease and no family history. This case bundle is variant-level only: it contains no proband phenotype, no family history, no parental testing, and no reported de novo occurrence for NM_004333.6:c.1799T>A. No de novo observation can therefore be counted and no points can be assigned; the criterion is not assessable rather than affirmatively excluded. Additional caveat for future assessment: this residue change (p.Val600Glu, reported as V599E in PMID:12068308) is a recurrent somatic BRAF mutation in cancer, so any apparently de novo result must be documented in germline (non-tumour) tissue with confirmed maternity and paternity before PS2 can be credited.
ClinGen RASopathy VCEP BRAF v2.3, PS2 (Applicable) - de novo with both maternity and paternity confirmed in a patient with the disease and no family history; point-based strength via ClinGen SVI Proposal for De Novo Criteria v1.1: 1 point = Moderate, 2 points = Strong, 4 points = Very Strong. No de novo point is assignable without proband/parental data.
The governing framework is the ClinGen RASopathy Expert Panel specification for BRAF v2.3, which does not use the generic PS4 prevalence rule for this gene. It requires point-based scoring of autosomal-dominant cases with phenotypic specifications: at least 1 point for supporting, 3 points for moderate, and 5 points for strong PS4, with full points awarded for RASopathy phenotypes and reduced points for cases with minimal phenotypic information. No qualifying case-level data exist in this bundle: there is no proband phenotype, no RASopathy case count, no point assignment, and no case-control or cohort enrichment analysis for the germline RASopathy phenotype. The exact-variant full texts and ClinVar submissions that do exist are predominantly somatic-origin tumour observations (melanoma, papillary thyroid carcinoma, colorectal carcinoma, low-grade astrocytoma, nonseminomatous germ cell tumour, vascular malformation), and the ACMG/AMP framework explicitly states it is not intended for interpretation of somatic variation, so somatic tumour mutation frequency cannot substitute for germline case-control enrichment under this VCEP. ClinVar's own record for this variant is a single-submitter laboratory record (7 laboratories Pathogenic, 2 Likely pathogenic, 2 Uncertain significance; 0 expert-panel submissions), and criterion leads must not be inferred from another source's final classification. PS4 therefore cannot be scored and is left not_assessed with the specific gaps recorded.
ClinGen RASopathy Expert Panel BRAF v2.3 PS4: strength adjustment using point-based scoring for autosomal dominant cases with phenotypic specifications; Supporting >=1 point, Moderate >=3 points, Strong >=5 points; full points with RASopathy phenotypes, reduced points for minimal phenotypic information.
The BRAF VCEP v2.3 defines PM5 as a count of DIFFERENT already-established [likely] pathogenic amino-acid changes at the SAME codon as the variant under review (1 such change = Moderate; at least 2 different such changes observed in at least 5 probands = Strong). The case's dedicated same-residue comparator collection (pm5_candidates.json) reviewed 8 candidate records, identified 0 same-residue candidates, and returned the recommendation 'no_useful_candidates_found' with an explicit instruction not to apply PM5 from that artifact alone. No other source in the bundle enumerates verified, individually citable pathogenic codon-600 substitutions: the hotspot artifact records V600 as a statistically significant hotspot but its row data was not parsed ('V600 hotspot row partially parsed'; warning 'Regex extraction partial; verify screenshot'), and no ClinVar comparator record for another codon-600 substitution was retrieved. PM5 therefore cannot be adjudicated without an ungrounded comparator claim, and is returned not_assessed with human review flagged.
Moderate: 1 [likely] pathogenic residue change at the same codon. Strong: >=2 different [likely] pathogenic residue changes at the same codon observed in >=5 probands.
The applicable framework is the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119), in which PM6 is Applicable and scored with the SVI de novo point system (0.5 points = Supporting, 1 point = Moderate, 2 points = Strong), used in conjunction with PS2 and with phenotype-dependent point allocation. PM6 requires an assumed de novo occurrence without confirmation of maternity and paternity. The case bundle contains no proband and no parental genotyping of any kind, so there is neither an observed nor an assumed de novo occurrence to score. Screening of the ClinVar submissions and of all seven fetched full texts found no report of this variant arising de novo in a patient. PM6 is therefore not assessable, not affirmatively excluded.
ClinGen RASopathy VCEP BRAF v2.3, PM6 (Applicable) - assumed de novo without confirmation of paternity and maternity; point-based strength via ClinGen SVI Proposal for De Novo Criteria v1.1: 0.5 points = Supporting, 1 point = Moderate, 2 points = Strong. No assumed de novo occurrence is available to score.
The applicable framework is the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119), in which PP1 is Applicable with meiosis-count thresholds (>=3 informative meioses = Supporting, >=5 = Moderate, >=7 = Strong) and the recommendation that segregation be shown in more than one family. PP1 requires co-segregation of the variant with disease in affected family members. This case bundle contains no family, no pedigree, no affected relative genotypes and therefore no informative meioses; segregation was not tested or reported by any source consulted. The criterion cannot be assessed at any strength. No lack of segregation is implied either, so the finding does not argue against pathogenicity.
ClinGen RASopathy VCEP BRAF v2.3, PP1 (Applicable) - co-segregation with disease in affected family members; >=3 informative meioses = Supporting, >=5 = Moderate, >=7 = Strong; segregation in more than one family recommended. Zero informative meioses available.
The BRAF VCEP v2.3 operationalises PP2 as a single gene-level test at Supporting strength: 'Missense z score is >3.09 in gnomAD'. No BRAF missense z score, and no gnomAD gene-constraint metric of any kind, is present in the supplied case evidence: the gnomAD artifacts contain only position-level allele counts for this variant, and the local hci_prior lookup returned found=false. Because the gene-level input the governing rule requires is absent, PP2 cannot be assessed; a missense z score recalled from memory is not acceptable as a substitute for a sourced value, and the rule was not broadened to generic 'missense mechanism' reasoning.
Supporting: Missense z score is >3.09 in gnomAD.
The applicable framework is the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF v2.3 (cspec doc 643243119), in which BS4 is Applicable at Benign Strong strength and, unlike generic ACMG/AMP, 'Requires only one informative meiosis'. BS4 requires demonstration that the variant does not segregate with disease in affected members of a family. No family, pedigree, meiosis or affected-relative genotype is present in this case bundle, and no source consulted reports non-segregation for NM_004333.6:c.1799T>A. The criterion is therefore not assessable and must not be applied as benign evidence.
ClinGen RASopathy VCEP BRAF v2.3, BS4 (Applicable, Benign Strong) - lack of segregation in affected members of a family; requires only one informative meiosis. No informative meiosis available, so BS4 cannot be applied.
BP2 is applicable under the BRAF VCEP framework, which requires an alternative molecular cause of a RASopathy in the same gene, with phenotype consistent with the expected severity, and uses phase-sensitive evidence such as an additional pathogenic variant in trans or cis. The case bundle contains no affected-proband or family-level observation documenting a second BRAF pathogenic variant, no cis/trans phase determination, and no alternative molecular cause in the same gene. Therefore BP2 cannot be assessed from the available evidence.
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. Supporting: ≥ (-1) Point; Moderate: ≥ (-2) Points; Strong: ≥ (-4) Points.
Under the governing BRAF RASopathy VCEP v2.3, BP5 is awarded through negative point-based scoring: points are given for an alternative molecular cause of a RASopathy in a different gene (and/or in conjunction with BP2) with a phenotype consistent with the expected RASopathy severity, or for a phenotype inconsistent with RASopathy that is fully explained by a different causative variant (for example on WES). Thresholds are at least -1 point (supporting), -2 points (moderate) and -4 points (strong). The bundle contains no individual-level molecular or phenotypic data for the case under review - no co-occurring causative variant, no RASopathy phenotype severity description, and no negative point assignment - so the criterion cannot be scored and is left not_assessed rather than being asserted as absent. Nothing in the reviewed literature or ClinVar submissions documents an alternate molecular basis for this variant.
ClinGen RASopathy Expert Panel BRAF v2.3 BP5: negative point-based scoring for an alternative molecular cause of a RASopathy in a different gene and/or for a phenotype inconsistent with RASopathy fully explained by a different causative variant; Supporting >=-1 point, Moderate >=-2 points, Strong >=-4 points.
Not applicable under the governing ClinGen RASopathy Expert Panel BRAF v2.3 specification, which marks PVS1 as not applicable. The normalized preferred-transcript consequence is the single amino-acid substitution p.(Val600Glu), not a predicted loss-of-function variant.
ClinGen RASopathy Expert Panel BRAF v2.3: PVS1 is not applicable.
PS1 requires the variant under assessment to share its amino-acid change with a previously established pathogenic variant produced by a DIFFERENT nucleotide change (BRAF VCEP v2.3 PS1: 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in BRAF and RAF1.'). NM_004333.6:c.1799T>A is itself the canonical, extensively catalogued BRAF record conferring NP_004324.2:p.(Val600Glu) (ClinVar variation 13961, Pathogenic; the same c.1799T>A nucleotide change), so there is no independent same-amino-acid comparator for PS1 to operate on and the criterion is not applicable to this variant. The VCEP's paralogous-residue branch (analogous positions in BRAF/RAF1) could not be evaluated: the VCEP RAF-Alignment workbook supplies its alignment only as embedded images with no extractable residue mapping, and no registry source documents an established pathogenic RAF1 change at the position analogous to BRAF Val600. Because the CSPEC wording ('regardless of nucleotide change') can also be read as making the identical p.(Val600Glu) record sufficient, this disposition is flagged for human confirmation; PS1 is not used to infer any other criterion.
Strong: 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 applicable ClinGen RASopathy VCEP specification for BRAF Version 2.3 designates PM3 as not applicable. The framework specifies autosomal dominant inheritance for the BRAF RASopathy context, so the recessive-disease in-trans evidence model for PM3 is not used.
Not applicable.
The governing BRAF RASopathy VCEP v2.3 specification explicitly designates PP4 as not applicable and routes phenotype-specificity evidence into PS4, stating 'Not applicable, see PS4.' Because the gene-specific framework removes this criterion, PP4 cannot be awarded here regardless of phenotype information. No case phenotype data exist in the bundle in any event.
ClinGen RASopathy Expert Panel BRAF v2.3: PP4 Not Applicable ('Not applicable, see PS4.').
The applicable BRAF VCEP Version 2.3 framework explicitly marks BS3 as Not Applicable. Therefore, no benign functional evidence criterion is assigned, regardless of the absence of a benign assay result in the reviewed evidence.
BRAF VCEP Version 2.3: BS3 Not Applicable.
The BRAF VCEP v2.3 states that BP1 'has contraindications for use with RASopathies' and restricts it to truncating variants (nonsense, frameshift, canonical splice site, initiation codon, whole-gene or multi-exon deletion) in genes without an established loss-of-function correlation to disease, given the gain-of-function RASopathy mechanism. NM_004333.6:c.1799T>A is a missense substitution (NP_004324.2:p.(Val600Glu)) in exon 15, not a truncating or canonical splice variant, so the variant class the rule targets is not met and BP1 is not applicable.
Supporting: 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.
Not applicable under the governing ClinGen RASopathy Expert Panel BRAF v2.3 specification, which marks BP3 as not applicable. Independently, this is a single-residue substitution rather than an in-frame protein-length change in a repetitive region.
ClinGen RASopathy Expert Panel BRAF v2.3: BP3 is not applicable.
BP7 as specified by the governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) applies to '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', and the specification adds that the rule is also applicable to intronic positions (except canonical splice sites) or non-coding variants. NM_004333.6:c.1799T>A is a coding missense substitution, p.(Val600Glu), not a synonymous, intronic or non-coding variant, so BP7 is not applicable. The available SpliceAI result (max delta 0.007, no predicted splice impact) does not create BP7 applicability for a missense change, and it is not being double-counted with the REVEL-based PP3 call.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC BP7: synonymous/intronic (non-canonical)/non-coding variant with no predicted splice impact and non-conserved nucleotide (not applicable to missense variants)
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 |
|---|
| South Asian1 / 91,076 | 1.1e-05 |
| European (non-Finnish)1 / 1,179,108 | 8.5e-07 |
| South Asian1 / 30,612 | 3.3e-05 |
This variant is present in gnomAD v4.1 (AF= 1.23999e-06; MAF= 0.00012%, 2/1612922 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09798e-05; MAF= 0.00110%, 1/91076 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.97994e-06; MAF= 0.00040%, 1/251260 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
NM_004333.6:c.1799T>A is a missense substitution, NP_004324.2:p.(Val600Glu) (BRAF V600E), so it is adjudicated on the missense protein-impact path. The governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) states for PP3: 'For missense variants: REVEL >= 0.7', at Pathogenic Supporting strength. The local REVEL v1.3 lookup returns REVEL = 0.931 for this variant, which exceeds the 0.7 VCEP cutoff, so PP3 is met at supporting strength. BayesDel (0.335473) was not used because no verified published calibration for these criteria is available to this pipeline. The SpliceAI result was deliberately NOT used as support: a spliced-path score cannot clear a missense variant's protein-level effect, and no predicted splice impact is not evidence about the substituted amino acid.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC PP3: for missense variants, REVEL >= 0.7 -> PP3 supporting
NM_004333.6:c.1799T>A (p.Val600Glu) is a missense variant, so BP4 is assessed on the missense path. The governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) BP4 rule is 'For missense variants: REVEL <= 0.3'. The local REVEL v1.3 score is 0.931, which is far above 0.3, so the BP4 benign-supporting threshold is not met. The splice sub-rule of BP4 ('predicted outcome is negligible or does not match disease mechanism') cannot be used to meet BP4 for this missense variant, and in any case the CSPEC requires its in-silico criteria to be counted only once per variant; the same REVEL score that supports PP3 cannot also support BP4. BP4 is therefore not met.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC BP4: for missense variants, REVEL <= 0.3 -> BP4 supporting (not satisfied)
BP7 as specified by the governing ClinGen RASopathy Expert Panel BRAF specification (v2.3, doc 643243119) applies to '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', and the specification adds that the rule is also applicable to intronic positions (except canonical splice sites) or non-coding variants. NM_004333.6:c.1799T>A is a coding missense substitution, p.(Val600Glu), not a synonymous, intronic or non-coding variant, so BP7 is not applicable. The available SpliceAI result (max delta 0.007, no predicted splice impact) does not create BP7 applicability for a missense change, and it is not being double-counted with the REVEL-based PP3 call.
ClinGen RASopathy VCEP (BRAF) v2.3 CSPEC BP7: synonymous/intronic (non-canonical)/non-coding variant with no predicted splice impact and non-conserved nucleotide (not applicable to missense variants)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.931. BayesDel score = 0.335473.
7 paper records listed. 6 cited in the classification.
All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation.
Location Abstract; Results paragraphs describing mutation frequency and functional characterization; Table 1; Table 2; Table 3
Context Somatic mutation screening of 545 cancer cell lines and 378 primary cancers/short-term cultures; BRAF kinase cascade assays and ERK1/2 phosphorylation assays in transiently transfected COS cells; NIH3T3 focus-transformation assays; RAS-neutralizing antibody and MEK-inhibitor treatment of cancer cell lines.
Tumors with mutant BRAF and those with receptor tyrosine kinase (RTK) activation have similar levels of phosphorylated ERK, but only the former depend on ERK signaling for proliferation.
Location Abstract and Results (MEK/ERK-dependent transcriptional output in BRAF-mutant tumours)
Context Tumour cell-line and xenograft signalling studies defining MEK/ERK-dependent gene expression signatures in BRAF-mutant versus RTK-driven tumours.
In BRAFV600E tumors, RAS is not activated, thus transactivation is minimal and ERK signaling is inhibited in cells exposed to RAF inhibitors.
Location Results, opening paragraph; Results, paragraph beginning 'Nevertheless, the clinical utility of these inhibitors…'; clinical implications section
Context Cell-based MEK/ERK signalling assays in 293H and HT29 cells expressing endogenous or introduced BRAFV600E with RAF inhibitors (PLX4032/PLX4720) versus a MEK inhibitor, plus discussion of a phase I PLX4032 trial in metastatic melanoma.
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.
Location Results, paragraph beginning “BRAF mutations were identified”
Context Sequenom MassARRAY hotspot mutation screen of paediatric solid-tumour samples, with identified mutations verified by bidirectional Sanger sequencing.
The most common mutation (*90 %) is the V600E substitution, located in the kinase domain of the protein (exon 15). BRAF mutations and KRAS mutations are mutually exclusive, so the former are never found in KRAS-mutated tumours and vice versa. They are associated with the presence of high microsatellite instability (MSI-H) induced by acquired defects in MMR enzyme function [13, 31]. In other contexts, particularly in advanced disease, the presence of BRAF mutations is associated with a worse prognosis [13, 31, 33, 34, 38, 42, 43].
Location Molecular markers of metastatic CRC, subsection “BRAF,” page 731; subsection “BRAF testing,” page 735
Context Consensus review of biomarker testing in colorectal carcinoma; the paper states that BRAF V600E can be studied by sequencing but does not report a variant-specific cohort or functional assay.
The following approach to evaluating evidence for a variant is intended for interpretation of variants observed in patients with suspected inherited (primarily Mendelian) disorders in a clinical diagnostic laboratory setting. It is not intended for the interpretation of somatic variation, pharmacogenomic (PGx) variants, or variants in genes associated with multigenic non-Mendelian complex disorders.
Location Proposed Criteria for Interpretation of Sequence Variants (PS2, PM6, PP1, BS4 definitions), page 6 and criteria tables
Context Consensus recommendation / guideline document for sequence variant interpretation (no cohort, assay or family data).
The V599EΔB-RAF kinase domain was ∼500-fold more active than WTΔB-RAF (data not shown). Thus the Glu substitution for Val599 exerts its stimulatory effect on kinase activity within the context of the kinase domain of B-RAF, and this suggests that B-RAF activation is not simply a release from the autoinhibitory restraints conferred by the N-terminal region. Moreover, because we dephosphorylated the purified B-RAF kinase domain, the high activity of V599EΔB-RAF indicates that activation segment phosphorylation is not required for the kinase activity of the mutant protein.
Results and Discussion, “Expression, Purification, and Enzyme Activity of WT B-RAF and V599E B-RAF Kinase Domains”
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
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= 1.23999e-06; MAF= 0.00012%, 2/1612922 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09798e-05; MAF= 0.00110%, 1/91076 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.97994e-06; MAF= 0.00040%, 1/251260 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (7 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Uncertain significance (2 clinical laboratories). (ClinVarID = 13961)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.931. BayesDel score = 0.335473.
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; COSV56056643, n = 31792 times).
This variant lies in a statistically significant hotspot.