Starting
Initialising…
0%
BRAF
Final classification
VUS
BRAF c.770A>G · p.Gln257Arg
BRAF

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

Gene
BRAF
Transcript
NM_001354609.1
HGVS · transcript:coding
NM_001354609.1:c.770A>G
Consequence
N/A
GRCh38
chr7:140801502 T>C
GRCh37
chr7:140501302 T>C
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PP5 supporting, PM1 moderate, PP3 supporting, PS3 moderate; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PP5 supporting, PM1 moderate, PP3 supporting, PS3 moderate; no rule matched the adjudicated criteria.
Classification rationale
PP5PM1PP3PS3 VUS
BRAF c.770A>G

The BRAF c.770A>G (p.Gln257Arg) variant has been reported in ClinVar as pathogenic, including expert panel review.1 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%.2 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.3 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 0.21.4

PP5 + PM1 + PP3 + PS3 VUS
3 vcep_svi_rasopathy_vcep_v2_approved_functional_studiescspec ↗
4 revelbayesdelspliceai ↗cspec ↗
Gene diagram · NM_001354609.1 · variants mapped to exon structure
BRAF NM_001354609.1
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This 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).
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,613,978
      0 hom
      European (non-Finnish)
      1 / 1,179,918
      8.5e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      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).
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.21). REVEL score = 0.838. BayesDel score = 0.476355.
      Functional / OncoKB screenshot
      Functional 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 ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:16439621
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:16474404
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:19376813
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:33019809
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots