Variant classification summary

NM_004333.5:c.2107G>A

BRAF · NP_004324.2:p.(Glu703Lys) · NM_004333.5

GRCh37: chr7:140439632 C>T · GRCh38: chr7:140739832 C>T

Gene: BRAF Transcript: NM_004333.5

Final call

VUS

PM2 supporting PP2 supporting

Variant details

Gene

BRAF

Transcript

NM_004333.5

Protein

NP_004324.2:p.(Glu703Lys)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_004333.5:c.2107G>A (p.Glu703Lys) is a missense variant in BRAF exon 17, within the C-terminal lobe of the kinase domain but outside all VCEP-specified PM1 critical functional domains (P-loop AA 459-474, CR3 activation segment AA 594-627).

2

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength under the RASopathy VCEP.

3

BRAF has a gnomAD missense Z-score >3.09, meeting PP2 at supporting strength, consistent with low tolerance for benign missense variation in this gene.

4

The REVEL score of 0.579 does not meet the VCEP thresholds for PP3 (≥0.7) or BP4 (≤0.3), and SpliceAI predicts no splice impact (max delta 0.06). Computational evidence is indeterminate.

5

No functional data exists for p.Glu703Lys in any VCEP-approved assay (BRAF Kinase, MEK Activation, ERK Activation); the variant is not listed in the SVI functional studies spreadsheet. OncoKB reports Unknown Oncogenic Effect.

6

No same-codon pathogenic comparator exists at residue 703 (PM5), no de novo observations have been reported (PS2/PM6), no case-control or segregation data is available (PS4/PP1), and no prior pathogenic assertion for E703K exists (PS1).

7

ClinVar reports a single submitter classifying the variant as Uncertain Significance (Variation ID 4856330, criteria provided, single submitter). PP5 and BP6 are not applicable under this VCEP.

8

The only met criteria are PM2_Supporting and PP2_Supporting. No pathogenic criteria at moderate, strong, or very strong level are met. Under the RASopathy VCEP combination rules, this evidence is insufficient to classify the variant as Pathogenic or Likely Pathogenic, and insufficient benign evidence exists to classify as Benign or Likely Benign. 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	PVS1 is not applicable under the ClinGen RASopathy VCEP for BRAF (version 2.3.0); the variant is a missense substitution (c.2107G>A, p.Glu703Lys) and does not meet the null-variant criteria of nonsense, frameshift, or canonical splice site alteration.	cspec
PS1	Not met	PS1 requires the same amino acid change to have been previously established as pathogenic. The variant p.Glu703Lys has not been established as pathogenic; ClinVar reports a single submitter classifying it as Uncertain Significance. No prior pathogenic assertion exists for E703K in the literature or ClinVar.	clinvar
PS2	Not met	No de novo occurrence of NM_004333.5:c.2107G>A has been reported. The literature and ClinVar submissions contain no confirmed de novo observations for this variant.
PS3	Not met	No functional data exists for p.Glu703Lys in any VCEP-approved assay (BRAF Kinase Activity, MEK Activation Assay, ERK Activation Assay). The variant is not listed among validation controls or tested variants in the SVI-RASopathy-VCEP-V2-Approved-Functional-Studies spreadsheet. OncoKB reports Unknown Oncogenic Effect with no variant-specific functional evidence.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies oncokb
PS4	Not met	No case-control data or proband counts are available for NM_004333.5:c.2107G>A. The variant has not been reported in affected individuals beyond the single ClinVar submission, which lacks phenotypic details. Insufficient evidence to meet any PS4 point threshold under the RASopathy VCEP.	clinvar
PS5	N/A	PS5 is not defined in the ClinGen RASopathy VCEP criteria set for BRAF (version 2.3.0). No VCEP rule exists for this criterion.	cspec
PM1	Not met	PM1 under the RASopathy VCEP is restricted to exon 6, exon 11, the P-loop (amino acids 459-474), and the CR3 activation segment (amino acids 594-627). The variant p.Glu703Lys lies in exon 17 within the C-terminal lobe of the kinase domain, outside all VCEP-specified PM1 domains. It is also not located in a statistically significant cancer hotspot per cancerhotspots.org.	cspec
PM2	Met	The variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0, meeting the VCEP PM2_Supporting rule requiring absence from population controls.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 under the RASopathy VCEP requires at least one [likely] pathogenic residue change at the same codon. No other missense change at codon 703 has been reported as pathogenic or likely pathogenic in ClinVar. The only variant at this codon is E703K itself (VUS).	pm5_candidates clinvar
PM6	Not met	No assumed de novo observation (without confirmed parentage) has been reported for NM_004333.5:c.2107G>A. No proband data with parental genotypes is available.
PP1	Not met	No co-segregation data is available for NM_004333.5:c.2107G>A. No family studies with this variant have been reported.
PP2	Met	BRAF has a gnomAD missense Z-score >3.09, meeting the VCEP PP2 rule. BRAF is a well-established gene with low tolerance for benign missense variation, and missense variants are a common mechanism of disease in RASopathies.	cspec
PP3	Not met	The REVEL score for this variant is 0.579, below the VCEP PP3 threshold of REVEL ≥0.7. SpliceAI predicts no splice impact (max delta score 0.06). Computational evidence does not support a deleterious effect.	revel spliceai bayesdel
PP4	N/A	PP4 is designated as Not Applicable by the ClinGen RASopathy VCEP for BRAF (version 2.3.0). The VCEP directs users to PS4 instead.	cspec
PP5	N/A	PP5 is designated as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. This criterion is not for use under the RASopathy VCEP framework.	cspec
BA1	Not met	BA1 under the RASopathy VCEP requires a gnomAD filtering allele frequency ≥0.05%. The variant is absent from all gnomAD populations, falling far below this threshold.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 under the RASopathy VCEP requires a gnomAD filtering allele frequency ≥0.025%. The variant is absent from all gnomAD populations, falling below this threshold.	gnomad_v2 gnomad_v4
BS2	Not met	No observations of this variant in healthy adult individuals have been reported. No data available to satisfy BS2 point-based scoring under the RASopathy VCEP.
BS3	N/A	BS3 is designated as Not Applicable by the ClinGen RASopathy VCEP for BRAF (version 2.3.0).	cspec
BS4	Not met	No segregation data is available to demonstrate lack of segregation in affected family members. The VCEP requires only one informative meiosis for BS4, but no family data exists for this variant.
BP1	N/A	BP1 under the RASopathy VCEP applies only to truncating variants (nonsense, frameshift, canonical splice sites, initiation codon, whole-gene or multi-exon deletions) in genes where the disease mechanism is gain-of-function. NM_004333.5:c.2107G>A is a missense variant and does not meet the truncating variant requirement for BP1.	cspec
BP2	Not met	No evidence of an alternative molecular cause of a RASopathy in the same gene has been identified. No data available to satisfy BP2 point-based scoring.
BP4	Not met	BP4 under the RASopathy VCEP requires a REVEL score ≤0.3 for missense variants. The REVEL score for this variant is 0.579, which does not meet the BP4 threshold.	revel spliceai
BP5	Not met	No evidence of an alternative molecular cause of a RASopathy in a different gene has been identified. No data available to satisfy BP5 point-based scoring.
BP6	N/A	BP6 is designated as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. This criterion is not for use under the RASopathy VCEP framework.	cspec
BP7	N/A	BP7 under the RASopathy VCEP applies to synonymous (silent) variants and intronic positions outside canonical splice sites. NM_004333.5:c.2107G>A is a missense variant (p.Glu703Lys) and does not qualify for BP7.	cspec
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions. This variant is a single-nucleotide substitution, not an in-frame indel.
PM3	N/A	PM3 applies to recessive disorders (detected in trans with a pathogenic variant). RASopathies are autosomal dominant; this criterion is not applicable.
PM4	N/A	PM4 applies to protein length changes from in-frame deletions/insertions or stop-loss variants. This variant is a missense substitution and does not alter protein length.

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