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KRAS
Final classification
VUS
KRAS c.34_35delinsTGTGC · p.Gly12delinsCysAla
KRAS

This variant resides at codon 12 within the P-loop domain (AA 10-17), a critical functional domain per RASopathy VCEP specifications. Codon 12 is a well-established mutational hotspot with no benign variation. The variant lies in a statistically significant hotspot.

Gene
KRAS
Transcript
NM_033360.3
HGVS · transcript:coding
NM_033360.3:c.34_35delinsTGTGC
Consequence
N/A
GRCh38
chr12:25245350 CC>GCACA
GRCh37
chr12:25398284 CC>GCACA
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 was evaluated deterministically with applied criteria: PM1 moderate, PM2 supporting, PM4 moderate; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM1 moderate, PM2 supporting, PM4 moderate; no rule matched the adjudicated criteria.
Classification rationale
PM1PM2PM4 VUS
KRAS c.34_35delinsTGTGC

This variant resides at codon 12 within the P-loop domain (AA 10-17), a critical functional domain per RASopathy VCEP specifications. Codon 12 is a well-established mutational hotspot with no benign variation. The variant lies in a statistically significant hotspot.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting rarity in the general population.2 The variant is an in-frame deletion-insertion that alters protein length (p.Gly12delinsCysAla) in a non-repetitive region, consistent with a potential gain-of-function effect in the RAS/MAPK pathway.3 No variant-specific functional studies, de novo observations, case reports, or segregation data were identified in the available literature or databases. OncoKB classifies this variant as Oncogenic with gain-of-function effect.4 Insufficient evidence exists to reach a definitive classification under the RASopathy VCEP v2.3.0 framework. Met criteria: PM1 (Moderate), PM2 (Supporting), PM4 (Moderate). Key data gaps include absence of functional studies, patient phenotype data, and segregation analysis.5

PM1 + PM2 + PM4 VUS
Gene diagram · NM_033360.3 · variants mapped to exon structure
KRAS NM_033360.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 13 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant affects codon 12 within the P-loop domain (amino acids 10-17), a critical and well-established functional domain per the RASopathy VCEP supplementary table. Codon 12 is a known mutational hotspot with no benign variation in this region. Hotspot analysis confirms this residue is statistically significant.
P-loop domain includes AA 10-17 per VCEPcodon 12 is a well-established hotspotvariant position confirmed as statistically significant hotspot
PM2 supporting Pathogenic
This variant is absent from all population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Per RASopathy VCEP v2.3.0, PM2 is applied at Supporting strength when the variant is absent from gnomAD controls.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0
PM4 moderate Pathogenic
This is an in-frame deletion-insertion (c.34_35delinsTGTGC) resulting in a protein length change (p.Gly12delinsCysAla). KRAS has no known repetitive regions per the RASopathy VCEP. PM4 is applied at Moderate strength per VCEP rule: 'No known repetitive areas in gene. Use as described.'
In-frame delins at codon 12 alters protein lengthno repetitive regions in KRAS per VCEP
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change as a previously established pathogenic variant.
PS2 No de novo observations for this specific variant were identified in the available literature or ClinVar submissions.
PS3 No variant-specific functional studies for NM_033360.3:c.34_35delinsTGTGC were identified.
PS4 No patient case data or case-control studies involving this variant were identified.
PM6 No assumed de novo observations for this variant were identified.
PP1 No co-segregation data for this variant was identified in the available literature.
PP3 VCEP PP3 applies to missense variants with REVEL ≥0.7 or splicing impact matching disease mechanism.
Benign
BA1 RASopathy VCEP BA1 threshold is gnomAD filtering allele frequency ≥0.05%.
BS1 RASopathy VCEP BS1 threshold is gnomAD filtering allele frequency ≥0.025%.
BS2 No data regarding observation of this variant in healthy adult individuals was available.
BS4 No segregation data was available to assess lack of segregation in affected family members.
BP2 No data regarding observation of this variant in trans with a pathogenic variant or cis with a pathogenic variant was available.
BP5 No data regarding an alternative molecular cause of RASopathy was available.
N/A · 11 PVS1 · PM5 · PP2 · PP4 · PP5 · BS3 · BP1 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
Functional / OncoKB screenshot
Functional Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: 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 not previously been reported in somatic cancers (COSMIC).
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 · 1 PMID not cited in assessment
24642870 ↗ Characterization of rare transforming KRAS mutations in sporadic colorectal cancer. ONCOKB