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NRAS
Final classification
Pathogenic
NRAS c.34G>T · p.Gly12Cys
NRAS

NM_002524.4:c.34G>T (p.Gly12Cys) in NRAS is a missense variant affecting codon 12 in the P-loop (AA 10-17), a critical GTP-binding domain recognized by the RASopathy VCEP.

Gene
NRAS
Transcript
NM_002524.4
HGVS · transcript:coding
NM_002524.4:c.34G>T
Consequence
N/A
GRCh38
chr1:114716127 C>A
GRCh37
chr1:115258748 C>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule7 (1 Pathogenic.Strong + 2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PS1 strong, PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting; maps to Pathogenic.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule7 (1 Pathogenic.Strong + 2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PS1 strong, PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting; maps to Pathogenic.
Classification rationale
PS1PM1PM2PM5PP3 Pathogenic
NRAS c.34G>T

NM_002524.4:c.34G>T (p.Gly12Cys) in NRAS is a missense variant affecting codon 12 in the P-loop (AA 10-17), a critical GTP-binding domain recognized by the RASopathy VCEP.1 The p.Gly12Cys amino acid change is a well-established pathogenic alteration in NRAS and homologous RAS genes, meeting PS1 at Strong strength.2 The variant lies within the P-loop functional domain (PM1, Moderate) and represents a missense change at a codon where other pathogenic missense variants are established (PM5, Moderate).3 The variant is absent from all gnomAD population databases, meeting PM2 at Supporting strength.4 REVEL score of 0.773 supports a deleterious effect, meeting PP3 at Supporting strength.5 No de novo, cosegregation, case-count, or functional assay data from VCEP-approved platforms were available for this variant; PS2, PS3, PS4, PM6, PP1, BS2, BS4, BP2, and BP5 remain unassessed.

PS1 + PM1 + PM2 + PM5 + PP3 Pathogenic
Gene diagram · NM_002524.4 · variants mapped to exon structure
NRAS NM_002524.4
Fetching transcript structure from UCSC…
Applied criteria · 5 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
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      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 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (2 clinical laboratories). (ClinVarID = 40468)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.773. BayesDel score = 0.298187.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54736487, n = 273 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      26619011 ↗ Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. ONCOKB
      28572459 ↗ AACR Project GENIE: Powering Precision Medicine through an International Consortium. ONCOKB
      33637626 ↗ Differential Outcomes in Codon 12/13 and Codon 61 NRAS-Mutated Cancers in the Phase II NCI-MATCH Trial of Binimetinib in Patients with NRAS-Mutated Tumors. ONCOKB
      9219684 ↗ The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. ONCOKB
      26037647 ↗ Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations. CLINVAR
      6092966 ↗ Biological properties of human c-Ha-ras1 genes mutated at codon 12. CLINVAR
      19681119 ↗ RAS signaling dysregulation in human embryonal Rhabdomyosarcoma. CLINVAR
      20963938 ↗ CEBPA-Associated Familial Acute Myeloid Leukemia (AML). CLINVAR