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LYFE SCIENCES
Project: HERA
NM_001354609.1:c.770A>G
p.Gln257Arg  ·  BRAF
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Classification rationale
1

The BRAF c.770A>G (p.Gln257Arg) variant has been reported in ClinVar as pathogenic, including expert panel review.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and is present only once in gnomAD v4.1 (1/1,613,978 alleles; AF 0.00006%), which is below the BS1 threshold of 0.025% and the BA1 threshold of 0.05%.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

In VCEP-approved functional studies, Q257R showed abnormal results in MEK activation, ERK activation, and BRAF kinase activity assays, consistent with a damaging gain-of-function effect.

cspec ↗
4

Computational evidence supports a deleterious missense effect, with REVEL 0.838 above the PP3 threshold of 0.7, a positive BayesDel score of 0.476355, and SpliceAI showing only a low predicted splice effect with a maximum delta score of 0.21.

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
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1Absent from gnomAD v2.1.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 6.19587e-07; MAF= 0.00006%, 1/1613978 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47517e-07; MAF= 0.00008%, 1/1179918 alleles, homozygotes = 0).
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (32 clinical laboratories) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.21). REVEL score = 0.838. BayesDel score = 0.476355.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueQ257
Hotspots ↗