Starting
Initialising…
0%
KRAS
Final classification
Likely Pathogenic
KRAS c.34G>C · p.Gly12Arg
KRAS

The KRAS c.34G>C (p.Gly12Arg, p.G12R) variant has been observed in somatic cancers in COSMIC (COSV55497582; n=1720) and has been reported in ClinVar with pathogenic and likely pathogenic clinical submissions.

Gene
KRAS
Transcript
NM_033360.2
HGVS · transcript:coding
NM_033360.2:c.34G>C
Consequence
N/A
GRCh38
chr12:25245351 C>G
GRCh37
chr12:25398285 C>G
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework; Rule14 applies.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework; Rule14 applies.
Classification rationale
PM5PM1PM2PP3 Likely Pathogenic
KRAS c.34G>C

The KRAS c.34G>C (p.Gly12Arg, p.G12R) variant has been observed in somatic cancers in COSMIC (COSV55497582; n=1720) and has been reported in ClinVar with pathogenic and likely pathogenic clinical submissions.1 This variant is absent from population controls, with 0/249272 alleles in gnomAD v2.1 and no observation in gnomAD v4.1, which supports PM2 and argues against BA1 and BS1.2 Available functional evidence is consistent with an activating KRAS effect, and OncoKB classifies this variant as oncogenic with gain-of-function, but the curated RASopathy VCEP materials did not provide sufficient approved variant-specific assay evidence to apply PS3.3 This missense change affects codon 12 within the KRAS P-loop domain, and computational data are consistent with a damaging missense effect, with REVEL 0.821 and no predicted splice disruption by SpliceAI (maximum delta score 0.00).4

PM5 + PM1 + PM2 + PP3 Likely Pathogenic
3 oncokb ↗vcep_s_v_i___r_a_s_o_p_a_t_h_y___v_c_e_p___v_2___a_p_p_r_o_v_e_d___f_u_n_c_t_i_o_n_a_l___s_t_u_d_i_e_sPMID:23455880 ↗PMID:26037647 ↗PMID:32792368 ↗
4 cspec ↗spliceai ↗vcep_a_l_i_g_n_m_e_n_t___w_i_t_h___p_m_1___d_o_m_a_i_n_s___p_p_t_x
Gene diagram · NM_033360.2 · variants mapped to exon structure
KRAS NM_033360.2
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 · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/249272 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16042 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / 249,272
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (3 clinical laboratories) and as Likely pathogenic (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB classifies this variant as Oncogenic; biological effect: Gain-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55497582, n = 1720 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots