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Variant interpretation report

KRAS c.531_533del, p.(Lys180del)

NM_001369787.1:c.531_533del NP_001356716.1:p.(Lys180del) View identifiers
Classification
Benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About KRAS

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 3
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 3
BA1Stand alone
BA1 · stand alone

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.

BS1Strong
BS1 · strong

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.

BP6Supporting
BP6 · supporting

Expert panel ClinGen RASopathy Variant Curation Expert Panel classified as Benign.

Recorded classification: 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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
1,732 / 1,610,758 alleles

gnomAD v4.1: 1,732 / 1,610,758 alleles. Recorded AF 0.00107527. Recorded homozygote count 2.

gnomAD v2.1

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.

SpliceAI score
0.290 maximum delta

Recorded SpliceAI maximum delta score: 0.290. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
Functional evidence
Statement recorded

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

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 3

BA1 Stand aloneThis 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. Details ▾Hide ▴
Rule
GnomAD filtering allele frequency ≥0.05%.
Evidence considered
  • gnomAD v2.1 overall AF 0.05904%
  • highest subpopulation AF 0.10364%
  • gnomAD v4.1 overall AF 0.10753%
  • highest subpopulation AF 0.13901%
  • RASopathy VCEP BA1 threshold 0.05%
Sources
BS1 StrongThis 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. Details ▾Hide ▴
Rule
GnomAD filtering allele frequency ≥0.025%.
Evidence considered
  • gnomAD v2.1 overall AF 0.05904%
  • highest subpopulation AF 0.10364%
  • gnomAD v4.1 overall AF 0.10753%
  • highest subpopulation AF 0.13901%
  • RASopathy VCEP BS1 threshold 0.025%
Sources
BP6 SupportingExpert panel ClinGen RASopathy Variant Curation Expert Panel classified as Benign. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks BP6 not applicable
  • ClinVar expert panel classification
Sources

Not met · 5 · evaluated, threshold not reached

PS4 Available evidence does not show enrichment of this variant in affected individuals. The variant is classified as Benign in ClinVar with expert panel review, is not reported in COSMIC, and is present in gnomAD at frequencies above benign thresholds, so PS4 is not met. Details ▾Hide ▴
Rule
Supporting ≥1 point; Moderate ≥3 points; Strong ≥5 points.
Evidence considered
  • ClinVar expert panel benign classification
  • No COSMIC result found
  • Population frequency exceeds benign thresholds
Still missing
  • No case-control or affected-versus-control enrichment study for this exact variant was identified.
Sources
PM1 This variant does not fall within the KRAS RASopathy VCEP PM1 domains. The affected residue is Lys180, which is outside the specified P-loop (amino acids 10-17), switch I (25-40), switch II (57-64), and SAK (145-156) regions, so PM1 is not met. Details ▾Hide ▴
Rule
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).
Evidence considered
  • Affected residue Lys180
  • PM1 domains limited to amino acids 10-17
  • 25-40
  • 57-64
  • and 145-156
Sources
PM2 This variant is not absent from controls. It is present in gnomAD v2.1 at 0.05904% overall and in gnomAD v4.1 at 0.10753% overall, so the PM2 requirement for absence from controls is not met. Details ▾Hide ▴
Rule
The variant must be absent from controls (gnomAD).
Evidence considered
  • Variant present in gnomAD v2.1
  • Variant present in gnomAD v4.1
  • RASopathy VCEP PM2 requires absence from controls
Sources
PP3 Computational evidence does not support PP3 for this variant. REVEL and BayesDel are not available for this in-frame deletion, and SpliceAI shows a maximum delta score of 0.29, which does not by itself establish a predicted splice effect matching the KRAS RASopathy disease mechanism. Details ▾Hide ▴
Rule
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
Evidence considered
  • SpliceAI max delta score 0.29
  • No REVEL score available
  • No BayesDel score available
Sources
BP1 BP1 in this RASopathy framework is reserved for truncating variants in genes without an established loss-of-function disease correlation. This variant is an in-frame deletion and does not meet that condition, so BP1 is not met. Details ▾Hide ▴
Rule
Use for truncating variants in genes without established LOF correlation to disease.
Evidence considered
  • Variant consequence is an in-frame deletion
  • not truncating
Sources

Not assessed · 9 · no assessment recorded

PS2 No confirmed de novo occurrence with sufficient parentage information was identified for this variant, so PS2 cannot be assessed from the available evidence. Details ▾Hide ▴
Rule
Very Strong 4 points; Strong 2 points; Moderate 1 point.
Evidence considered
  • No de novo evidence identified in reviewed materials
Still missing
  • No documented de novo case for this exact variant was identified.
  • Parental testing and maternity/paternity confirmation were not available.
Sources
PS3 No approved variant-specific functional assay result was identified for this exact KRAS in-frame deletion. The reviewed KRAS functional-study materials list approved assay types for the gene, but they do not provide a variant-specific approved assay result for p.Lys180del that would support PS3. Details ▾Hide ▴
Rule
Two or more different approved assays (Moderate); one approved assay (Supporting).
Evidence considered
  • RASopathy VCEP approved assay list reviewed
  • OncoKB did not identify variant-specific reviewed functional evidence
Still missing
  • No exact-variant approved assay result was identified.
  • No direct PMID-backed functional study for p.Lys180del was retrieved.
Sources
cspec ↗vcep_svi_rasopathy_vcep_v2_approved_functional_studiesoncokb ↗
PM4 This variant is an in-frame single-amino-acid deletion, but the available evidence does not establish that it should be counted as PM4-level pathogenic evidence in this case. The reviewed materials do not provide variant-specific evidence showing that this protein-length change has a disease-causing effect independent of the strong benign population data. Details ▾Hide ▴
Rule
No known repetitive areas in gene. Use as described.
Evidence considered
  • Protein consequence p.(Lys180del)
  • Strong benign population signal
  • ClinVar expert panel benign classification
Still missing
  • Variant-specific evidence supporting PM4 application was not identified.
  • No direct VCEP case-level explanation for PM4 use or non-use for this exact variant was available in the reviewed sources.
Sources
PM6 No presumed de novo report without full confirmation was identified for this variant, so PM6 cannot be assessed from the available evidence. Details ▾Hide ▴
Rule
Strong 2 points; Moderate 1 point; Supporting 0.5 points.
Evidence considered
  • No PM6-type inheritance evidence identified in reviewed materials
Still missing
  • No presumed de novo case for this exact variant was identified.
Sources
PP1 No segregation data were identified for this variant. There is no evidence of co-segregation across informative meioses, so PP1 cannot be assessed. Details ▾Hide ▴
Rule
Supporting ≥3 informative meioses; Moderate ≥5 informative meioses; Strong ≥7 informative meioses.
Evidence considered
  • No segregation evidence identified in reviewed materials
Still missing
  • No family segregation report for the exact variant was identified.
Sources
BS2 Population data show this variant in gnomAD, including 2 homozygotes in v4.1, but the reviewed materials do not provide the case-based point assessment required by the KRAS RASopathy VCEP BS2 rule. BS2 therefore remains unassessed here. Details ▾Hide ▴
Rule
Strong -4 points; Supporting -1 point.
Evidence considered
  • gnomAD v4.1 reports 2 homozygotes
  • BS2 is a point-based VCEP rule
Still missing
  • No VCEP point-based BS2 assessment for unaffected individuals was available.
Sources
BS4 No informative non-segregation data were identified for this variant, so BS4 cannot be assessed from the available evidence. Details ▾Hide ▴
Rule
Requires only one informative meiosis.
Evidence considered
  • No BS4-type family data identified in reviewed materials
Still missing
  • No family non-segregation report for the exact variant was identified.
Sources
BP2 No phased occurrence with another variant and no VCEP point-based BP2 evidence were identified for this variant, so BP2 cannot be assessed from the available data. Details ▾Hide ▴
Rule
Strong ≥(-4) points; Moderate ≥(-2) points; Supporting ≥(-1) point.
Evidence considered
  • BP2 is a point-based VCEP rule
  • No companion-variant evidence identified
Still missing
  • No in trans or in cis companion-variant evidence was identified.
  • No point-based BP2 assessment was available.
Sources
BP5 No alternative molecular diagnosis or phenotype-discordant explanation was identified for this variant, so BP5 cannot be assessed from the available evidence. Details ▾Hide ▴
Rule
Strong ≥(-4) points; Moderate ≥(-2) points; Supporting ≥(-1) point.
Evidence considered
  • BP5 is a point-based VCEP rule
  • No alternate molecular explanation identified
Still missing
  • No alternative molecular cause with a point-based BP5 assessment was identified.
Sources
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 VCEPPVS1 is not applicable in this KRAS RASopathy framework, and the variant-specific PVS1 review found that this change is an in-frame deletion rather than a nonsense, frameshift, or canonical splice variant. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks PVS1 not applicable
  • Variant consequence is p.(Lys180del)
  • an in-frame deletion
Sources
cspec ↗pvs1_gene_contextpvs1_variant_assessment
PS1 N/APS1 is a same-amino-acid-change rule for variants producing an already established pathogenic amino acid substitution. This variant is an in-frame deletion, not an alternate nucleotide change causing the same amino acid substitution, so PS1 is not applicable. Details ▾Hide ▴
Rule
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Evidence considered
  • Variant consequence is an amino-acid deletion
  • not a missense substitution
Sources
PM3 VCEPPM3 is not applicable in the KRAS RASopathy VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks PM3 not applicable
Sources
PM5 N/AThe KRAS RASopathy VCEP uses classic same-residue missense PM5 logic. This variant is an in-frame deletion rather than a missense change, and the PM5 candidate review marked it as not applicable for this variant class. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PM5 mode is classic same-residue missense
  • Variant class is not missense-like
Sources
cspec ↗pm5_candidates
PP2 VCEPPP2 is not applicable in the KRAS RASopathy VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks PP2 not applicable
Sources
PP4 VCEPPP4 is not applicable in the KRAS RASopathy VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks PP4 not applicable
Sources
PP5 VCEPPP5 is not used in this VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks PP5 not applicable
Sources
BS3 VCEPBS3 is not applicable in the KRAS RASopathy VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks BS3 not applicable
Sources
BP3 VCEPBP3 is not applicable in the KRAS RASopathy VCEP framework. Details ▾Hide ▴
Evidence considered
  • KRAS RASopathy VCEP marks BP3 not applicable
Sources
BP4 N/ABP4 is specified by this framework for missense variants with REVEL 0.3 or lower. This variant is an in-frame deletion rather than a missense change, and no framework-specific benign computational rule was identified for this variant class. Details ▾Hide ▴
Rule
For missense variants: REVEL ≤0.3.
Evidence considered
  • Variant consequence p.(Lys180del)
  • BP4 rule specified for missense variants
Sources
BP7 N/ABP7 is intended for synonymous, intronic, or non-coding variants with no predicted splice effect. This variant is an in-frame coding deletion, so BP7 is not applicable. Details ▾Hide ▴
Rule
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.
Evidence considered
  • Variant consequence p.(Lys180del)
  • BP7 rule applies to synonymous/intronic/non-coding variants
Sources

Identifiers

Gene
KRAS
Transcript
NM_001369787.1
Coding (HGVS c.)
NM_001369787.1:c.531_533del
Protein (HGVS p.)
NP_001356716.1:p.(Lys180del)
GRCh38
chr12:25209828 TTTC>T
GRCh37
chr12:25362762 TTTC>T
ClinVar
45129

Gene diagram

Every interpreted variant in KRAS, mapped onto the exon structure of NM_001369787.1. Select a row to find it on the plot.

KRASNM_001369787.1
Fetching transcript structure from UCSC…
gnomAD v4.1 1,732 / 1,610,758 alleles AF 0.00108 · 2 homozygotes · FAF 0.00133
gnomAD v2.1 166 / 281,144 alleles AF 0.00059 · 0 homozygotes · FAF 0.0009

By genetic ancestry

gnomAD v4.1

AF 0.0011 · 1732 / 1,610,758 alleles · 2 hom · FAF 0.0013
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
0 alternate alleles recorded in 2 other groups: Amish, Middle Eastern.

gnomAD v2.1

AF 0.00059 · 166 / 281,144 alleles · 0 hom · FAF 0.0009
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
0 alternate alleles recorded in 1 other group: Ashkenazi Jewish.

Statements

gnomAD v4.1

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.

gnomAD v2.1

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.

SpliceAI and Pangolin

SpliceAI acceptor lossat +83 bp
0.000
SpliceAI acceptor gainat -17 bp
0.000
SpliceAI donor lossat -17 bp
0.090
SpliceAI donor gainat +14 bp
0.290
Pangolin splice lossmagnitude shown
-0.080
Pangolin splice gain
0.180

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 Computational evidence does not support PP3 for this variant. REVEL and BayesDel are not available for this in-frame deletion, and SpliceAI shows a maximum delta score of 0.29, which does not by itself establish a predicted splice effect matching the KRAS RASopathy disease mechanism. Details ▾Hide ▴
Rule
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
Evidence considered
  • SpliceAI max delta score 0.29
  • No REVEL score available
  • No BayesDel score available
Sources
BP4 N/ABP4 is specified by this framework for missense variants with REVEL 0.3 or lower. This variant is an in-frame deletion rather than a missense change, and no framework-specific benign computational rule was identified for this variant class. Details ▾Hide ▴
Rule
For missense variants: REVEL ≤0.3.
Evidence considered
  • Variant consequence p.(Lys180del)
  • BP4 rule specified for missense variants
Sources
BP7 N/ABP7 is intended for synonymous, intronic, or non-coding variants with no predicted splice effect. This variant is an in-frame coding deletion, so BP7 is not applicable. Details ▾Hide ▴
Rule
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.
Evidence considered
  • Variant consequence p.(Lys180del)
  • BP7 rule applies to synonymous/intronic/non-coding variants
Sources

Statement

In silico

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.

Recorded publications

  • A systematic approach to assessing the clinical significance of genetic variants.
    Duzkale H et al. · 2013
    No paper-specific finding is recorded.
    PMID 24033266 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    Richards S et al. · 2015
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.
    Bodian DL et al. · 2014
    No paper-specific finding is recorded.
    PMID 24728327 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    Nykamp K et al. · 2017
    No paper-specific finding is recorded.
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

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.

ClinVar

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)

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.29).

Functional

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

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.