About BRAF
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
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.No gene-level summary was recorded for this case.
The recorded framework is ClinGen BRAF VCEP v2.3.0. 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.
BRAF is a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease. The RASopathy VCEP applies PP2 at supporting strength when the gene's missense z-score exceeds 3.09 in gnomAD. BRAF has a well-established high missense constraint (missense z-score significantly > 3.09), consistent with a gene where missense variation is a common disease mechanism in RASopathies.
The VCEP applies PP3 at supporting strength for missense variants when REVEL score is at least 0.7. The REVEL score for NM_004333.5:c.1447A>G (p.Lys483Glu) is 0.973, well above the threshold, indicating a strong in silico prediction of deleterious effect. SpliceAI predicts no splicing impact (max delta = 0.00), consistent with an amino-acid-level deleterious effect.
No benign criterion marked as applied in the recorded assessment.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 1 / 1,613,408 alleles. Recorded AF 6.19806e-07. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.9789e-06; MAF= 0.00040%, 1/251326 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89419e-05; MAF= 0.00289%, 1/34552 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
1 Uncertain significance. ClinVar API review status: criteria provided, single submitter.
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; COSV56236813, n = 19 times).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRAF VCEP v2.3.0, with the data and sources behind each one.
29 criteria with recorded statuses: 2 met · 16 not met · 0 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_004333.5:c.1447A>G (p.Lys483Glu) is a missense variant in BRAF, a gene where missense variants are a common mechanism of RASopathy disease. REVEL score of 0.973 strongly predicts a deleterious effect on protein function, satisfying PP3 at supporting strength. The gene's missense z-score exceeds 3.09 in gnomAD, meeting PP2 at supporting strength. The variant is present at extremely low frequency in gnomAD (1/251,326 alleles in v2.1; 1/1,613,408 alleles in v4.1) but is not absent, so PM2 (supporting) is not met under the VCEP requirement for complete absence. The variant lies outside VCEP-defined functional domains (P-loop AA 459-474, CR3 AA 594-627) and no pathogenic comparator exists at codon 483, so PM1 and PM5 are not met. No de novo, segregation, or case-control data are available for germline RASopathy. Functional data from the cancer literature classifies K483E as a Class 3 BRAF mutation (kinase-impaired, activates ERK via CRAF transactivation), but this has not been tested in VCEP-approved assays. No benign criteria are met. With two supporting pathogenic criteria (PP2, PP3) and no criteria at moderate or strong level, the variant does not meet any VCEP pathogenic or likely pathogenic classification rule. Per VCEP framework rules, the variant remains a Variant of Uncertain Significance.
No criteria match.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
Every interpreted variant in BRAF, mapped onto the exon structure of NM_004333.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Admixed American1 / 60,012 | 1.7e-05 |
| Admixed American1 / 34,552 | 2.9e-05 |
This variant is present in gnomAD v4.1 (AF= 6.19806e-07; MAF= 0.00006%, 1/1613408 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66633e-05; MAF= 0.00167%, 1/60012 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.9789e-06; MAF= 0.00040%, 1/251326 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89419e-05; MAF= 0.00289%, 1/34552 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.973. BayesDel score = 0.579862.
3 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
pBabe-bleo-Flag-BRAF-WT and pBABEbleo-FLAG-BRAF-K483E were generated by gene synthesis and cloning (GenScript, Piscataway, NJ, USA).
Methods: Transfection and retroviral transduction section; plasmid construction details
K483E | 3 | 14
Table 1 (Class 3 mutations listing); Results section
Dela Cruz et al. reported that BRAF K483E expression potentiated ERK activation although it harbors a catalytically dead kinase domain.
Results section (Drug responses of PDOs, paragraph on encorafenib and binimetinib responses); Discussion
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= 6.19806e-07; MAF= 0.00006%, 1/1613408 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66633e-05; MAF= 0.00167%, 1/60012 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.9789e-06; MAF= 0.00040%, 1/251326 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89419e-05; MAF= 0.00289%, 1/34552 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1418218)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.973. BayesDel score = 0.579862.
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 does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56236813, n = 19 times).
This variant does not lie in a statistically significant hotspot.