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LYFE SCIENCES
Project: HERA
NM_001354609.1:c.1796C>G
p.Thr599Arg  ·  BRAF
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Classification rationale
1

The BRAF c.1796C>G (p.Thr599Arg) variant has been reported in ClinVar as pathogenic, including an expert panel pathogenic classification, and is also represented in curated cancer variant resources.

clinvar ↗ oncokb ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, which supports rarity in population reference datasets.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

In approved functional studies, this variant was classified as pathogenic in both MEK activation and ERK activation assays, supporting abnormal MAPK pathway signaling consistent with the disease mechanism.

cspec ↗ PMID:19206169 ↗
4

In silico evidence does not meet the BRAF RASopathy thresholds for PP3 or BP4 because REVEL is 0.359, SpliceAI predicts no significant splice impact with a maximum delta score of 0.00, and BayesDel is 0.308415.

spliceai ↗ cspec ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (4 clinical laboratories) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.359. BayesDel score = 0.308415.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56167356, n = 2 times).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueT599
Hotspots ↗