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KRAS
Final classification
VUS
KRAS c.35_37delinsATT · p.Gly12_Gly13delinsAspCys
KRAS

NM_033360.3:c.35_37delinsATT (p.Gly12_Gly13delinsAspCys) is an in-frame deletion-insertion in exon 2 of KRAS, altering codons 12 and 13 within the P-loop domain (AA 10-17), a critical functional domain per the ClinGen RASopathy Expert Panel specifications v2.3.0.

Gene
KRAS
Transcript
NM_033360.3
HGVS · transcript:coding
NM_033360.3:c.35_37delinsATT
Consequence
N/A
GRCh38
chr12:25245348 CAC>AAT
GRCh37
chr12:25398282 CAC>AAT
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.35_37delinsATT

NM_033360.3:c.35_37delinsATT (p.Gly12_Gly13delinsAspCys) is an in-frame deletion-insertion in exon 2 of KRAS, altering codons 12 and 13 within the P-loop domain (AA 10-17), a critical functional domain per the ClinGen RASopathy Expert Panel specifications v2.3.0.1 The variant is absent from gnomAD population databases (v2.1, v4.1, and Canada), meeting PM2 at supporting strength per the RASopathy VCEP.2 The variant lies within the P-loop domain (AA 10-17), a well-established functional domain, and the residue is a statistically significant hotspot, meeting PM1 at moderate strength.3 As an in-frame deletion-insertion in a non-repeat region, the variant meets PM4 at moderate strength per the RASopathy VCEP.4 No variant-specific functional studies, de novo observations, segregation data, or proband reports are available. The variant is absent from ClinVar and COSMIC.5 The combined evidence (PM1 moderate, PM4 moderate, PM2 supporting) yields 2 moderate and 1 supporting pathogenic criteria, which does not meet any RASopathy VCEP combination rule for Pathogenic or Likely Pathogenic. No benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS) under the ClinGen RASopathy Expert Panel specifications for KRAS v2.3.0.6

PM1 + PM2 + PM4 VUS
1 cspec ↗vcep_alignment_with_pm1_domains_pptx
6 cspec ↗final_classification_framework
Gene diagram · NM_033360.3 · variants mapped to exon structure
KRAS NM_033360.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 16 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant alters codons 12 and 13, which lie within the P-loop domain (AA 10-17), a critical and well-established functional domain in KRAS per the RASopathy VCEP. The P-loop is one of four designated PM1 domains (along with SW1, SW2, and SAK). Additionally, the residue is identified as a statistically significant hotspot by cancerhotspots.org.
VCEP defines P-loop (AA 10-17) as a critical functional domain eligible for PM1 at moderate strength. cancerhotspots.org independently confirms the residue is a statistically significant hotspot.
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the RASopathy VCEP requirement for PM2_Supporting (variant must be absent from controls).
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (genomes).
PM4 moderate Pathogenic
NM_033360.3:c.35_37delinsATT is an in-frame deletion-insertion in a non-repeat region resulting in a protein length change (replacement of two residues with two different residues). Per the RASopathy VCEP, PM4 applies at moderate strength because there are no known benign repetitive areas in RASopathy genes (BP3 is not applicable).
In-frame delins in a non-repeat region of KRAS.BP3 is not applicable per VCEP (no known benign repetitive areas in RASopathy genes).
Assessed · not applied
Pathogenic
PS1 This variant produces a complex double amino acid substitution p.(Gly12_Gly13delinsAspCys).
PS2 No de novo data are available for this variant.
PS3 No variant-specific functional data are available for NM_033360.3:c.35_37delinsATT.
PS4 No probands with this variant have been reported.
PM6 No assumed or confirmed de novo data are available for this variant.
PP1 No co-segregation data are available for this variant.
PP3 PP3 in the RASopathy VCEP requires REVEL ≥0.7 for missense variants.
Benign
BA1 The RASopathy VCEP BA1 threshold is gnomAD filtering allele frequency ≥0.05%.
BS1 The RASopathy VCEP BS1 threshold is gnomAD filtering allele frequency ≥0.025%.
BS2 No data are available regarding observation of this variant in healthy adult individuals.
BS4 No segregation data are available to assess lack of segregation in affected family members.
BP1 BP1 in the RASopathy VCEP applies to truncating variants (nonsense, frameshift, canonical splice site, initiation codon, entire gene or multi-exon deletion) in genes where LOF is not the disease mechanism.
BP2 No data are available regarding an alternative molecular cause of a RASopathy in the same gene.
BP4 BP4 in the RASopathy VCEP requires REVEL ≤0.3 for missense variants.
BP5 No data are available regarding an alternative molecular cause of a RASopathy in a different gene.
BP7 BP7 applies to synonymous (silent) variants with no predicted splice impact.
N/A · 8 PVS1 · PM5 · PP2 · PP4 · PP5 · BS3 · BP3 · BP6
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 Likely Oncogenic
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. KRAS, a GTPase which functions as an upstream regulator of the MAPK pathway, is frequently mutated in various cancer types including lung, colorectal
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