NM_004333.5:c.1330C>T

BRAF · NP_004324.2:p.(Arg444Trp) · NM_004333.5

GRCh37: chr7:140481478 G>A · GRCh38: chr7:140781678 G>A

Gene: BRAF Transcript: NM_004333.5

Final call

VUS

PM1 moderate PP2 supporting

Variant details

Gene

BRAF

Transcript

NM_004333.5

Protein

NP_004324.2:p.(Arg444Trp)

gnomAD AF

6.197215219369024e-07 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

PM1 (Moderate) is met: variant c.1330C>T (p.Arg444Trp) is located in exon 11, a VCEP-designated critical functional domain for BRAF per RASopathy VCEP v2.3.0.

PP2 (Supporting) is met: BRAF gnomAD missense Z-score exceeds 3.09, indicating strong purifying selection against missense variation, consistent with a gene where missense variants are a common mechanism of RASopathy disease.

PM2 is not met: the variant is present in gnomAD v2.1 (1/251,378) and v4.1 (1/1,613,628), which precludes application under the VCEP rule requiring absence from controls.

PP3 is not met: REVEL score (0.637) falls below the VCEP PP3 threshold of ≥0.7, and SpliceAI (max delta 0.09) predicts no splicing impact.

No benign criteria are met. BA1 and BS1 are not met (allele frequency far below population thresholds). BP4 is not met (REVEL 0.637 > 0.3 threshold).

Under RASopathy VCEP v2.3.0 combination rules, PM1_Moderate + PP2_Supporting does not satisfy any Pathogenic, Likely Pathogenic, Benign, or Likely Benign rule. The minimum for Likely Pathogenic requires either 1 Strong + 1 Moderate, or ≥3 Moderate, or 1 Moderate + ≥4 Supporting criteria. Final classification: Variant of Uncertain Significance (VUS).

PVS1, PS5, PP4, PP5, BS3, BP6 are not applicable under the VCEP framework. PS1, PS2, PS3, PS4, PM5, PM6, PP1, BS2, BS4, BP2, BP5 are not assessed due to absence of data. PM2, PP3, BA1, BS1, BP1, BP4, BP7 were assessed and not met.

Three ClinVar-attached PMIDs (25394175, 31829902, 35924163) were reviewed in full text; none mention NM_004333.5:c.1330C>T or p.Arg444Trp. These papers are clinical practice guidelines or consensus statements on cancer genetics referral and prostate cancer biomarkers and do not provide variant-specific evidence.

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	VCEP criterion not applicable (missense variant, not a null variant); confirmed by RASopathy VCEP v2.3.0 PVS1 applicability designation.	cspec
PS1	Not met	No evidence that Arg444Trp has been previously established as pathogenic via a different nucleotide change at the same residue. Not observed in any curated VCEP-approved assay or published pathogenic assertion.	cspec clinvar
PS2	Not assessed	No de novo data available for this variant. VCEP PS2 uses point-based de novo scoring requiring confirmed parentage and RASopathy phenotype.	cspec
PS3	Not assessed	Variant not tested in any VCEP-approved functional assays. No variant-specific functional data identified in the literature or functional studies spreadsheet.	cspec vcep_svi_rasopathy_vcep_v2_approved_functional_studies
PS4	Not assessed	No proband case counts or case-control data available. ClinVar submission audit yielded zero usable submissions for classification. VCEP PS4 uses a point-based scoring system requiring proband observations.	cspec clinvar
PS5	N/A	PS5 is not a criterion in the ClinGen RASopathy VCEP v2.3.0 framework. Under VCEP mode, only VCEP-defined criteria are applied.	cspec
PM1	Met	Variant c.1330C>T (p.Arg444Trp) is located in exon 11 (c.1315-1432), which is a VCEP-designated critical and well-established functional domain for BRAF. PM1 applied at Moderate strength per RASopathy VCEP v2.3.0 rule: '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]).'	cspec
PM2	Not met	VCEP PM2 rule requires the variant to be absent from gnomAD. This variant is present in gnomAD v2.1 (1/251,378 alleles, AF=3.98e-06) and gnomAD v4.1 (1/1,613,628 alleles, AF=6.20e-07). Presence in population databases precludes PM2 application under VCEP.	gnomad_v2 gnomad_v4 cspec
PM5	Not assessed	VCEP PM5 requires at least one [likely] pathogenic residue change at the same codon (444). No other pathogenic or likely pathogenic missense variant at codon 444 has been identified. PM5 candidates search returned zero candidates.	cspec pm5_candidates
PM6	Not assessed	No de novo data available. VCEP PM6 uses point-based de novo scoring; no de novo observations identified.	cspec
PP1	Not assessed	No cosegregation data available. VCEP PP1 requires informative meioses with RASopathy phenotype.	cspec
PP2	Met	BRAF gnomAD missense Z-score is well above 3.09, meeting VCEP PP2 criteria at Supporting strength. BRAF is highly constrained against missense variation in the general population, consistent with its role as a proto-oncogene where gain-of-function missense variants cause RASopathies.	cspec
PP3	Not met	VCEP PP3 requires REVEL score ≥ 0.7 for missense variants. REVEL score for p.Arg444Trp is 0.637, below the VCEP threshold. SpliceAI predicts no significant splice impact (max delta = 0.09).	revel spliceai cspec
PP4	N/A	VCEP PP4 is Not Applicable per RASopathy VCEP v2.3.0; see PS4 instead.	cspec
PP5	N/A	PP5 is not for use per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation and is designated 'Not Applicable' in RASopathy VCEP v2.3.0.	cspec
BA1	Not met	VCEP BA1 requires gnomAD filtering allele frequency ≥ 0.05%. Highest observed subpopulation AF is 2.89e-05 (0.0029%) in Admixed American (v2.1), far below the BA1 threshold.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	VCEP BS1 requires gnomAD filtering allele frequency ≥ 0.025%. The variant's maximum subpopulation AF (2.89e-05) is roughly 10-fold below this threshold.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	VCEP BS2 uses a point-based scoring system requiring observation in a healthy adult for a fully penetrant disorder. No data available to assess this criterion.	cspec
BS3	N/A	VCEP BS3 is Not Applicable per RASopathy VCEP v2.3.0.	cspec
BS4	Not assessed	VCEP BS4 assesses lack of segregation in affected family members. No segregation data available.	cspec
BP1	Not met	VCEP BP1 applies only to truncating variants (nonsense, frameshift, canonical splice, initiation codon, whole/multi-exon deletion) in genes where primarily missense GOF variants cause disease. This is a missense variant.	cspec
BP2	Not assessed	VCEP BP2 uses point-based scoring for an alternative molecular cause of a RASopathy in the same gene. No data on co-occurring variants available.	cspec
BP4	Not met	VCEP BP4 requires REVEL ≤ 0.3 for missense variants. REVEL score is 0.637, above this threshold. Multiple computational tools (REVEL 0.637, BayesDel 0.258) do not uniformly suggest no impact.	revel bayesdel spliceai cspec
BP5	Not assessed	VCEP BP5 uses point-based scoring for an alternative molecular cause of a RASopathy in a different gene. No data available.	cspec
BP6	N/A	BP6 is not for use per ClinGen Sequence Variant Interpretation VCEP Review Committee and is designated 'Not Applicable' in RASopathy VCEP v2.3.0.	cspec
BP7	Not met	VCEP BP7 applies to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. c.1330C>T is a missense variant (p.Arg444Trp), not a synonymous variant.	cspec

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