Starting
Initialising…
0%
BRAF
Final classification
VUS
BRAF c.622A>G · p.Ile208Val
BRAF

The BRAF c.622A>G (p.Ile208Val) variant has been reported in ClinVar with mostly likely benign laboratory submissions and an expert-panel uncertain significance classification, and published case-level data describe unaffected carriers and multiple individuals without findings consistent with a RASopathy.

Gene
BRAF
Transcript
NM_001354609.1
HGVS · transcript:coding
NM_001354609.1:c.622A>G
Consequence
N/A
GRCh38
chr7:140808049 T>C
GRCh37
chr7:140507849 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: BS2 supporting; 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: BS2 supporting; no rule matched the adjudicated criteria.
Classification rationale
BS2 VUS
BRAF c.622A>G

The BRAF c.622A>G (p.Ile208Val) variant has been reported in ClinVar with mostly likely benign laboratory submissions and an expert-panel uncertain significance classification, and published case-level data describe unaffected carriers and multiple individuals without findings consistent with a RASopathy.1 This variant is present in population databases at low frequency, including 4/282526 alleles in gnomAD v2.1 (0.00142%) and 24/1612526 alleles in gnomAD v4.1 (0.00149%), which is below the BRAF RASopathy BS1 threshold of 0.025% and below the BA1 threshold of 0.05%, but means PM2 is not met because the variant is not absent from controls.2 No approved variant-specific functional study was identified for p.Ile208Val in the reviewed RASopathy functional-study materials.3 Computational evidence does not meet the VCEP missense thresholds: REVEL is 0.318, which is below the PP3 cutoff of 0.7 but above the BP4 cutoff of 0.3, while SpliceAI predicts no meaningful splice effect with a maximum delta score of 0.01; the BayesDel score is -0.174758.4

BS2 VUS
3 vcep_svi_rasopathy_vcep_v2_approved_functional_studiescspec ↗
4 revelspliceai ↗bayesdelcspec ↗
Gene diagram · NM_001354609.1 · variants mapped to exon structure
BRAF NM_001354609.1
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 1.48835e-05; MAF= 0.00149%, 24/1612526 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.67165e-05; MAF= 0.00267%, 2/74860 alleles, homozygotes = 0); grpmax FAF= 1.145e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.4158e-05; MAF= 0.00142%, 4/282526 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.10236e-05; MAF= 0.00310%, 4/128934 alleles, homozygotes = 0); grpmax FAF= 7.02e-06.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0015% · 24 / 1,612,526
      0 hom · FAF 0.0011%
      African/African American
      2 / 74,860
      0.0027%
      European (non-Finnish)
      21 / 1,178,824
      0.0018%
      South Asian
      1 / 91,040
      0.0011%
      + 7 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0014% · 4 / 282,526
      0 hom · FAF 0.0007%
      European (non-Finnish)
      4 / 128,934
      0.0031%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Uncertain significance by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.318. BayesDel score = -0.174758.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRAF, an intracellular kinase, is frequently mutated in melanoma, thyroid and lung cancers among others.
      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
      1papers 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:29945942
      Found
      Structured finding pending for this record — see source link.
      Applied to
      BS2 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots