About KRAS
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen KRAS VCEP v2.3.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
No pathogenic criterion marked as applied in the recorded assessment.
This in-frame deletion is present in population databases above the KRAS RASopathy VCEP BA1 threshold. In gnomAD v2.1 the overall allele frequency is 0.05904% and the highest observed subpopulation frequency is 0.10364%; in gnomAD v4.1 the overall allele frequency is 0.10753% and the highest observed subpopulation frequency is 0.13901%. These values are above the BA1 threshold of 0.05%, supporting BA1.
This in-frame deletion is present in population databases above the KRAS RASopathy VCEP BS1 threshold. In gnomAD v2.1 the overall allele frequency is 0.05904% and the highest observed subpopulation frequency is 0.10364%; in gnomAD v4.1 the overall allele frequency is 0.10753% and the highest observed subpopulation frequency is 0.13901%. These values are above the BS1 threshold of 0.025%, supporting BS1.
Expert panel ClinGen RASopathy Variant Curation Expert Panel classified as Benign.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule17 (1 Benign.Stand Alone) with applied criteria: BA1 stand-alone benign, BS1 strong, BP6 supporting benign; maps to Benign.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 1,732 / 1,610,758 alleles. Recorded AF 0.00107527. Recorded homozygote count 2.
This variant is present in gnomAD v2.1 (AF= 0.000590445; MAF= 0.05904%, 166/281144 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00103636; MAF= 0.10364%, 133/128334 alleles, homozygotes = 0); grpmax FAF= 0.00089964.
Recorded SpliceAI maximum delta score: 0.290. Refer to the recorded PP3/BP4 rationale for interpretation.
10 Likely benign · 2 Benign · 1 Likely Benign.
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
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen KRAS VCEP v2.3.0, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 5 not met · 9 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The KRAS c.531_533del (p.Lys180del) variant has not been observed in COSMIC and is reported in ClinVar as Benign with expert panel review.
This variant is present in gnomAD v2.1 at 0.05904% overall and 0.10364% in the highest-frequency subpopulation, and in gnomAD v4.1 at 0.10753% overall and 0.13901% in the highest-frequency subpopulation, exceeding the KRAS RASopathy VCEP BA1 threshold of 0.05% and BS1 threshold of 0.025%.
Computational evidence does not support a disease-relevant splicing effect; SpliceAI showed a maximum delta score of 0.29, and no REVEL or BayesDel score was available for this in-frame deletion.
No criteria match.
GnomAD filtering allele frequency ≥0.05%.
GnomAD filtering allele frequency ≥0.025%.
Supporting ≥1 point; Moderate ≥3 points; Strong ≥5 points.
Applicable only to critical and well-established functional domains available in the supplementary table (P-loop [AA 10-17], SW1 [AA 25-40], SW2 [AA 57-64], SAK [AA 145-156]). Not applicable to specific amino acid residues (see PM5).
The variant must be absent from controls (gnomAD).
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
Use for truncating variants in genes without established LOF correlation to disease.
Very Strong 4 points; Strong 2 points; Moderate 1 point.
Two or more different approved assays (Moderate); one approved assay (Supporting).
No known repetitive areas in gene. Use as described.
Strong 2 points; Moderate 1 point; Supporting 0.5 points.
Supporting ≥3 informative meioses; Moderate ≥5 informative meioses; Strong ≥7 informative meioses.
Strong -4 points; Supporting -1 point.
Requires only one informative meiosis.
Strong ≥(-4) points; Moderate ≥(-2) points; Supporting ≥(-1) point.
Strong ≥(-4) points; Moderate ≥(-2) points; Supporting ≥(-1) point.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Strong: ≥2 different [likely] pathogenic residue changes at the same codon observed in ≥5 probands; Moderate: 1 [likely] pathogenic residue change at the same codon.
For missense variants: REVEL ≤0.3.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
Every interpreted variant in KRAS, mapped onto the exon structure of NM_001369787.1. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)1637 / 1,177,578 | 0.00142 hom |
| Remaining individuals38 / 62,358 | 0.00061 |
| African/African American31 / 74,928 | 0.00041 |
| Admixed American9 / 59,890 | 0.00015 |
| East Asian5 / 44,718 | 0.00011 |
| European (Finnish)6 / 63,958 | 9.4e-05 |
| South Asian5 / 90,844 | 5.5e-05 |
| Ashkenazi Jewish1 / 29,538 | 3.4e-05 |
| European (non-Finnish)133 / 128,334 | 0.001 |
| Remaining individuals4 / 7,176 | 0.00056 |
| African/African American13 / 24,820 | 0.00052 |
| Admixed American8 / 35,190 | 0.00023 |
| East Asian4 / 19,896 | 0.0002 |
| European (Finnish)2 / 25,052 | 8e-05 |
| South Asian2 / 30,352 | 6.6e-05 |
This variant is present in gnomAD v4.1 (AF= 0.00107527; MAF= 0.10753%, 1732/1610758 alleles, homozygotes = 2) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00139014; MAF= 0.13901%, 1637/1177578 alleles, homozygotes = 2); grpmax FAF= 0.00133394.
This variant is present in gnomAD v2.1 (AF= 0.000590445; MAF= 0.05904%, 166/281144 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00103636; MAF= 0.10364%, 133/128334 alleles, homozygotes = 0); grpmax FAF= 0.00089964.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
For missense variants: REVEL ≤0.3.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
SpliceAI predicts possible splice impact for this variant (max delta score = 0.29).
4 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.00107527; MAF= 0.10753%, 1732/1610758 alleles, homozygotes = 2) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00139014; MAF= 0.13901%, 1637/1177578 alleles, homozygotes = 2); grpmax FAF= 0.00133394.
This variant is present in gnomAD v2.1 (AF= 0.000590445; MAF= 0.05904%, 166/281144 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00103636; MAF= 0.10364%, 133/128334 alleles, homozygotes = 0); grpmax FAF= 0.00089964.
This variant has been reported in ClinVar as Likely benign (10 clinical laboratories) and as Benign (2 clinical laboratories) and as Likely Benign (1 clinical laboratory) and as Benign by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 45129)
SpliceAI predicts possible splice impact for this variant (max delta score = 0.29).
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
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.