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KRAS
Final classification
VUS
KRAS c.250A>G · p.Ile84Val
KRAS

BP4 (Supporting): REVEL 0.294 meets the VCEP pre-assigned <=0.3 threshold for missense variants.

Gene
KRAS
Transcript
NM_033360.3
HGVS · transcript:coding
NM_033360.3:c.250A>G
Consequence
N/A
GRCh38
chr12:25227274 T>C
GRCh37
chr12:25380208 T>C
Basis Variant of Uncertain Significance: only BP4 (Supporting) is met (REVEL 0.294 <= 0.3); no Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule is satisfied.
Variant of Uncertain Significance: only BP4 (Supporting) is met (REVEL 0.294 <= 0.3); no Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule is satisfied.
Classification rationale
BP4 VUS
KRAS c.250A>G

BP4 (Supporting): REVEL 0.294 meets the VCEP pre-assigned <=0.3 threshold for missense variants. Overall classification: VUS - only BP4 (Supporting) is applied, so no VCEP combination rule for Pathogenic, Likely Pathogenic, Benign, or Likely Benign is satisfied.

BP4 VUS
Gene diagram · NM_033360.3 · variants mapped to exon structure
KRAS NM_033360.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 21 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Met (Supporting): REVEL 0.294 meets the VCEP pre-assigned <=0.3 BP4 threshold for missense variants.
REVEL score 0.294 (source: revel, local REVEL v1.3 lookup) satisfies VCEP KRAS v2.3 BP4 threshold REVEL <= 0.3 (threshold source: ClinGen RASopathy VCEP KRAS v2.3, cspec doc 643243114) - 0.294 <= 0.3, BP4 met at Supporting.SpliceAI max delta score 0.04 (source: spliceai) predicts no significant splice impact; consistent with BP4 but not counted as an independent code.BayesDel score -0.119893 (source: bayesdel) not applied: no verified published threshold available to this pipeline, treated as insufficiently calibrated.
Assessed · not applied
Pathogenic
PS1 Not assessed: insufficient evidence was available to evaluate this criterion.
PS2 Not assessed: no confirmed de novo observation (no parental testing or confirmation), so zero points under the VCEP de novo rule.
PS3 Not assessed: no VCEP-approved functional assay result (RAS/MEK/ERK activation) exists for this exact variant.
PS4 Not assessed: no case-control or proband-cohort enrichment data exists; the single gnomAD allele (AF 6.2e-07) provides no enrichment signal.
PM1 Not assessed: insufficient evidence was available to evaluate this criterion.
PM2 Not met: the variant is present in gnomAD v4.1 as a single South Asian exome allele (AF 6.2e-07), failing the VCEP absent-from-controls requirement.
PM4 Not met: the change is missense (p.Ile84Val) with no protein length change - the 189-amino-acid protein is unchanged.
PM5 Not assessed: insufficient evidence was available to evaluate this criterion.
PM6 Not assessed: no de novo occurrence is reported with or without parental confirmation, so the VCEP point rule cannot be scored.
PP1 Not assessed: no segregation data - zero informative meioses versus the >=3 required for Supporting.
PP2 Not assessed: insufficient evidence was available to evaluate this criterion.
PP3 Not met: REVEL 0.294 versus the VCEP >=0.7 threshold for missense variants.
PP5 Not met: no ClinVar expert-panel Pathogenic/Likely pathogenic classification exists - only two laboratory VUS submissions (GeneDx, Labcorp).
Benign
BA1 Not met: gnomAD v4.1 AF 6.2e-07 (0.00006%) versus the >=0.05% BA1 threshold - roughly 800x below.
BS1 Not met: gnomAD v4.1 AF 6.2e-07 versus the >=0.025% BS1 threshold - roughly 400x below.
BS2 Not met: no homozygous carriers in any population database; the single heterozygous carrier is not healthy-adult BS2 evidence.
BS4 Not assessed: no affected individual tested and found not to carry the variant - not even one non-segregation meiosis exists.
BP1 Not assessed: insufficient evidence was available to evaluate this criterion.
BP2 Not assessed: no proband or family observations exist (no phase, co-occurrence, or carrier data), so zero VCEP points can be scored.
BP5 Not assessed: no case-level evidence of an alternate molecular basis for disease in a carrier of this variant.
BP6 Not met: no ClinVar expert-panel Benign/Likely benign classification exists - only two laboratory VUS submissions.
N/A · 6 PVS1 · PM3 · PP4 · BS3 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19642e-07; MAF= 0.00006%, 1/1613834 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09798e-05; MAF= 0.00110%, 1/91076 alleles, homozygotes = 0).
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
6.2e-05% · 1 / 1,613,834
0 hom
South Asian
1 / 91,076
0.0011%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
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 Uncertain significance (2 clinical laboratories). (ClinVarID = 1318518)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.294. BayesDel score = -0.119893.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
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 Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Rule & framework references · cited for criterion definitions, not variant evidence
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots