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 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.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.
This variant has been observed in multiple unrelated probands with cardio-facio-cutaneous (CFC) syndrome / RASopathy phenotype. It was identified among 8 BRAF mutations in 16 individuals from the original CFC cohort (Niihori et al. 2006). Nine independent clinical laboratories have submitted this variant as Pathogenic to ClinVar, and the ClinGen RASopathy VCEP has classified it as Pathogenic (VariationID 13965). The aggregate observation across multiple independent probands supports PS4 at a supporting level.
The variant c.736G>C lies within exon 6 (c.712-860), which is one of the critical and well-established functional domains defined by the ClinGen RASopathy VCEP v2.3.0 (along with exon 11, P-loop AA 459-474, and CR3 activation segment AA 594-627). Exon 6 encodes part of the cysteine-rich domain (CRD) critical for BRAF function. The variant is absent from gnomAD, meeting the requirement of no benign variation in the domain.
The variant is absent from gnomAD v2.1 and v4.1 population databases. Per the RASopathy VCEP v2.3.0, PM2 is applied at supporting strength when the variant is absent from gnomAD controls.
Niihori et al. 2006 (PMID:16474404) reported a de novo occurrence of BRAF c.736G>C (p.Ala246Pro) in a proband with CFC syndrome where both parents tested negative for the variant. However, formal maternity/paternity confirmation was not performed, satisfying PM6 (assumed de novo without confirmed parentage) at supporting level (0.5 points) per the RASopathy VCEP point-based scoring system.
BRAF has a high gnomAD missense z-score (well above 3.09), indicating strong constraint against missense variation in the general population. Missense variants are a common mechanism of disease for BRAF (gain-of-function in RASopathies). Per the RASopathy VCEP v2.3.0, PP2 is met at supporting strength when the gene's missense z-score exceeds 3.09 in gnomAD.
The REVEL score for this missense variant is 0.928, which exceeds the threshold of ≥0.7 specified by the RASopathy VCEP v2.3.0 for PP3 at supporting strength. Multiple in silico tools support a deleterious effect on protein function.
Expert panel ClinGen RASopathy Variant Curation Expert Panel classified as Pathogenic.
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: matched Rule15 (1 Pathogenic.Moderate + Pathogenic.Supporting >=4) with applied criteria: PS4 supporting, PM1 moderate, PM2 supporting, PM6 supporting, PP2 supporting, PP3 supporting, PP5 supporting; maps to Likely Pathogenic.
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.
Recorded SpliceAI maximum delta score: 0.050. Refer to the recorded PP3/BP4 rationale for interpretation.
9 Pathogenic.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has not previously been reported in somatic cancers (COSMIC).
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: 7 met · 5 not met · 7 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The BRAF c.736G>C (p.Ala246Pro) missense variant is absent from gnomAD population databases (PM2_Supporting).
The variant lies within exon 6, a critical functional domain defined by the ClinGen RASopathy VCEP v2.3.0 (PM1_Moderate).
The variant has been observed in multiple unrelated probands with cardio-facio-cutaneous syndrome, including the original CFC discovery cohort (Niihori et al. 2006), and is classified as Pathogenic by the ClinGen RASopathy VCEP in ClinVar with submissions from 9 clinical laboratories (PS4_Supporting).
A de novo occurrence was reported in a CFC proband with both parents negative, though without molecular confirmation of parentage (PM6_Supporting).
In silico predictions support a deleterious effect: REVEL score is 0.928, exceeding the VCEP threshold of 0.7 (PP3).
BRAF exhibits a high gnomAD missense z-score (>3.09), indicating constraint against missense variation, and missense variants are a common disease mechanism for RASopathies (PP2).
Functional studies by Wen et al. 2013 demonstrated that A246P increases Ras binding affinity relative to wild-type, consistent with a gain-of-function mechanism, though the assay is not in the VCEP-approved functional studies list (PS3 not assessed).
Under the ClinGen RASopathy VCEP v2.3.0 combination rules (Rule15: 1 moderate + ≥4 supporting → Likely Pathogenic), the variant meets PM1 (moderate) plus PM2_Supporting, PM6_Supporting, PS4_Supporting, PP2, and PP3 (5 supporting criteria), resulting in a classification of Likely Pathogenic.
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_001354609.1. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.928. BayesDel score = 0.460772.
8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
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.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
This variant has been reported in ClinVar as Pathogenic (9 clinical laboratories) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 13965)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.928. BayesDel score = 0.460772.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.