Variant classification summary

NM_004333.5:c.1447A>G

BRAF · NP_004324.2:p.(Lys483Glu) · NM_004333.5

GRCh37: chr7:140477861 T>C · GRCh38: chr7:140778061 T>C

Gene: BRAF Transcript: NM_004333.5

Final call

VUS

PP2 supporting PP3 supporting

Variant details

Gene

BRAF

Transcript

NM_004333.5

Protein

NP_004324.2:p.(Lys483Glu)

gnomAD AF

6.198060255062575e-07 (v4.1)

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_004333.5:c.1447A>G is a missense variant (p.Lys483Glu). PVS1 is defined for null variants (nonsense, frameshift, canonical splice sites) and is explicitly marked as not applicable by the ClinGen RASopathy VCEP for BRAF v2.3.0.	cspec
PS1	Not met	No evidence that the same amino acid change (p.Lys483Glu) has been previously established as pathogenic. K483E is classified as Variant of Uncertain Significance in ClinVar (single submitter, Invitae) and is not listed as pathogenic/likely pathogenic by any expert panel.	clinvar
PS2	Not met	No de novo observation data are available for this variant. No publications or clinical records report a confirmed de novo occurrence with maternity and paternity confirmed.
PS3	Not met	Functional data from the cancer literature demonstrates that BRAF K483E is a Class 3 mutation with impaired kinase activity that activates ERK signaling through CRAF transactivation (Owsley 2020, Kondo 2020). However, the ClinGen RASopathy VCEP PS3 criterion requires testing in VCEP-approved functional assays (MEK Activation, ERK Activation, or BRAF Kinase Activity assays as specified in the supplemental SVI-RASopathy-VCEP-V2-Approved-Functional-Studies spreadsheet). K483E has not been tested in any of these approved assays. The existing functional data, while informative, does not meet the VCEP PS3 evidence threshold.	PMID:33019809 PMID:33060766 PMID:27799065
PS4	Not met	No case-control data or proband counts are available in the context of RASopathy. The variant has been observed in somatic cancer cohorts (COSMIC: 19 samples; Owsley 2020: 14 occurrences), but these are cancer/somatic cases and do not constitute germline RASopathy proband evidence.	PMID:33019809
PS5	N/A	PS5 is not a criterion defined in the ClinGen RASopathy VCEP framework for BRAF v2.3.0, nor is it a standard ACMG/AMP 2015 criterion (Richards et al., PMID:25741868). No VCEP rule references PS5.	cspec
PM1	Not met	The VCEP defines PM1 as applicable only to specific functional domains: P-loop (AA 459-474) and CR3 activation segment (AA 594-627). The variant p.Lys483Glu (position 483) lies between these domains and is not within a VCEP-recognized critical functional domain. The variant is also not at a statistically significant hotspot (cancerhotspots.org).	cspec
PM2	Not met	The RASopathy VCEP requires the variant to be absent from gnomAD controls. NM_004333.5:c.1447A>G is present in gnomAD v2.1 (1/251,326 alleles; AF=3.98e-6) and gnomAD v4.1 (1/1,613,408 alleles; AF=6.20e-7). While at extremely low frequency, it is not absent, and thus the VCEP PM2 criterion is not satisfied.	gnomad_v2 gnomad_v4
PM5	Not met	No [likely] pathogenic missense variant at codon 483 other than the variant under assessment has been identified. ClinVar has no P/LP entries for any alternative amino acid change at position 483. No same-codon comparator variants were identified in the PM5 candidate search.	pm5_candidates
PM6	Not met	No assumed de novo data are available. No publications report this variant as a presumed de novo occurrence without confirmation of maternity and paternity.
PP1	Not met	No co-segregation data are available. The VCEP requires at least 3 informative meioses for supporting strength. No family studies or segregation analyses have been reported for this variant.
PP2	Met	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.	cspec
PP3	Met	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.	revel spliceai cspec
PP4	N/A	The ClinGen RASopathy VCEP marks PP4 as not applicable; see PS4 instead for phenotype-based evidence.	cspec
PP5	N/A	The ClinGen RASopathy VCEP explicitly states that PP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	The VCEP BA1 threshold is an allele frequency of at least 0.05% in gnomAD. The variant frequency is 0.0004% in gnomAD v2.1 and 0.00006% in gnomAD v4.1, far below the stand-alone benign threshold.	gnomad_v2 gnomad_v4
BS1	Not met	The VCEP BS1 threshold is an allele frequency of at least 0.025% in gnomAD. The variant frequency is far below this threshold (0.0004% in v2.1, 0.00006% in v4.1).	gnomad_v2 gnomad_v4
BS2	Not met	No data are available regarding observation of this variant in healthy adult individuals for a dominant disorder expected to be fully penetrant at an early age.
BS3	N/A	The ClinGen RASopathy VCEP lists BS3 as not applicable. The criterion for well-established functional studies showing no damaging effect is not implemented in this framework.	cspec
BS4	Not met	No segregation data are available to demonstrate lack of segregation in affected family members. The VCEP requires only one informative meiosis for strong benign evidence, but no such data exist.
BP1	N/A	The VCEP BP1 rule is specific to truncating variants in genes where the disease mechanism is gain-of-function. NM_004333.5:c.1447A>G is a missense variant (p.Lys483Glu), not a truncating variant. BP1 does not apply to missense variants in this framework.	cspec
BP2	Not met	No data are available regarding an alternative molecular cause of a RASopathy in the same gene (e.g., observation in trans with a pathogenic variant). The point-based scoring system requires at least -1 point for supporting strength, and no such evidence exists.
BP4	Not met	The VCEP BP4 threshold for missense variants is REVEL score at most 0.3. The REVEL score for p.Lys483Glu is 0.973, which is strongly in the pathogenic range and does not satisfy the benign computational evidence threshold. Additionally, SpliceAI predicts no splice impact (max delta 0.00), but the REVEL score alone precludes BP4 application.	revel spliceai cspec
BP5	Not met	No data are available regarding an alternative molecular cause of a RASopathy in a different gene, or a phenotype inconsistent with a RASopathy and fully explained by a different causative variant.
BP6	N/A	The ClinGen RASopathy VCEP explicitly states that BP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splice impact. NM_004333.5:c.1447A>G is a missense variant resulting in p.Lys483Glu and is not a synonymous variant.
BP3	N/A	Substitution variant; BP3 applies only to in-frame deletions/insertions in repetitive regions.
PM3	N/A	RASopathies are autosomal dominant disorders; PM3 (in trans with pathogenic for recessive disorders) is not applicable.
PM4	N/A	Substitution variant; PM4 applies only to protein-length-altering variants (in-frame indels, stop-loss).

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