Variant classification summary

NM_033360.3:c.35_37delinsATT

KRAS · NP_203524.1:p.(Gly12_Gly13delinsAspCys) · NM_033360.3

GRCh37: chr12:25398282 CAC>AAT · GRCh38: chr12:25245348 CAC>AAT

Gene: KRAS Transcript: NM_033360.3

Final call

VUS

PM1 moderate PM2 supporting PM4 moderate

Variant details

Gene

KRAS

Transcript

NM_033360.3

Protein

NP_203524.1:p.(Gly12_Gly13delinsAspCys)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

The variant is absent from gnomAD population databases (v2.1, v4.1, and Canada), meeting PM2 at supporting strength per the RASopathy VCEP.

3

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.

4

As an in-frame deletion-insertion in a non-repeat region, the variant meets PM4 at moderate strength per the RASopathy VCEP.

5

No variant-specific functional studies, de novo observations, segregation data, or proband reports are available. The variant is absent from ClinVar and COSMIC.

6

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.

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	The ClinGen RASopathy Expert Panel marks PVS1 as not applicable for KRAS (VCEP v2.3.0). The established disease mechanism for RASopathies is gain-of-function; loss-of-function variants are not a known mechanism, and PVS1 is calibrated for null variants in genes where LOF causes disease.	cspec
PS1	Not met	This variant produces a complex double amino acid substitution p.(Gly12_Gly13delinsAspCys). Although G12D and G13C are individually established pathogenic changes in KRAS, this variant is a unique in-frame delins that alters two residues simultaneously and does not match any single established pathogenic amino acid change. PS1 is calibrated for a variant producing the same single amino acid change as a known pathogenic variant.	cspec
PS2	Not met	No de novo data are available for this variant. The variant has not been reported in any proband, and no parental testing data exist.
PS3	Not met	No variant-specific functional data are available for NM_033360.3:c.35_37delinsATT. The RASopathy VCEP has approved KRAS functional assays (RAS Activation Assay, ERK Activation Assay) that include G12V as a validated pathogenic control, but this exact variant has not been directly tested in any published functional study. Domain-level inference from G12 missense variant data does not satisfy PS3's requirement for variant-specific functional evidence.	vcep_svi_rasopathy_vcep_v2_approved_functional_studies
PS4	Not met	No probands with this variant have been reported. The variant is absent from ClinVar and no case reports exist in the literature. PS4 requires proband counts to meet point-based scoring thresholds (≥1 point for supporting).	clinvar
PS5	N/A	PS5 is not specified in the KRAS RASopathy VCEP criteria v2.3.0. Same-codon comparisons are handled by PM5 in this framework.	cspec
PM1	Met	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.	cspec vcep_alignment_with_pm1_domains_pptx
PM2	Met	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).	gnomad_v2 gnomad_v4 gnomad_canada
PM4	Met	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).	cspec
PM5	N/A	PM5 is defined for missense variants at the same codon where a different pathogenic missense has been established. This variant is an in-frame deletion-insertion (delins), not a missense substitution. The PM5 candidates pipeline confirms the variant class is not missense-like.	pm5_candidates
PM6	Not met	No assumed or confirmed de novo data are available for this variant. No probands have been reported.
PP1	Not met	No co-segregation data are available for this variant. The RASopathy VCEP requires at least 3 informative meioses for supporting-level PP1.
PP2	N/A	PP2 is marked as not applicable by the KRAS RASopathy VCEP because the missense z-score is <3.09 in gnomAD.	cspec
PP3	Not met	PP3 in the RASopathy VCEP requires REVEL ≥0.7 for missense variants. REVEL and BayesDel scores are not available for this indel variant. SpliceAI predicts no significant splice impact (max delta score 0.01), and splice alteration does not match the gain-of-function disease mechanism. No computational evidence supports a deleterious effect.	spliceai
PP4	N/A	PP4 is marked as not applicable by the KRAS RASopathy VCEP; see PS4 for patient phenotype data.	cspec
PP5	N/A	PP5 is marked as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Additionally, the variant is absent from ClinVar and no reputable source has classified it.	cspec clinvar
BA1	Not met	The RASopathy VCEP BA1 threshold is gnomAD filtering allele frequency ≥0.05%. The variant is absent from all gnomAD datasets (v2.1, v4.1, and Canada).	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The RASopathy VCEP BS1 threshold is gnomAD filtering allele frequency ≥0.025%. The variant is absent from all gnomAD datasets (v2.1, v4.1, and Canada).	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data are available regarding observation of this variant in healthy adult individuals. The RASopathy VCEP requires point-based scoring based on phenotypic specifications.
BS3	N/A	BS3 is marked as not applicable by the KRAS RASopathy VCEP.	cspec
BS4	Not met	No segregation data are available to assess lack of segregation in affected family members. The RASopathy VCEP requires only one informative meiosis for BS4 at strong level.
BP1	Not met	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. This variant is an in-frame deletion-insertion, not a truncating variant.	cspec
BP2	Not met	No data are available regarding an alternative molecular cause of a RASopathy in the same gene. The RASopathy VCEP requires point-based scoring for BP2.
BP3	N/A	BP3 is marked as not applicable by the KRAS RASopathy VCEP because there are no known benign repetitive areas in RASopathy genes.	cspec
BP4	Not met	BP4 in the RASopathy VCEP requires REVEL ≤0.3 for missense variants. REVEL and BayesDel scores are not available for this indel variant. SpliceAI predicts no significant splice impact (max delta 0.01), but the VCEP BP4 rule is calibrated specifically for REVEL thresholds on missense variants, not SpliceAI on indels.	spliceai
BP5	Not met	No data are available regarding an alternative molecular cause of a RASopathy in a different gene. The RASopathy VCEP requires point-based scoring for BP5.
BP6	N/A	BP6 is marked as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Additionally, the variant is absent from ClinVar and no reputable source has classified it as benign.	cspec clinvar
BP7	Not met	BP7 applies to synonymous (silent) variants with no predicted splice impact. This variant is an in-frame deletion-insertion that changes two amino acids (Gly12Asp and Gly13Cys), and is therefore not a synonymous variant.

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