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LYFE SCIENCES
Project: HERA
NM_001369787.1:c.451-14T>C
p.?  ·  KRAS
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Classification rationale
1

The KRAS c.451-14T>C (p.?) variant has been reported in ClinVar as Likely Benign, including an expert-panel likely benign assertion from the ClinGen RASopathy Variant Curation Expert Panel.

clinvar ↗
2

This variant is present in population databases, including gnomAD v2.1 at 0.00398% (11/276052 alleles) and gnomAD v4.1 at 0.01100% (175/1591272 alleles), which is above the PM2 absence requirement but below the KRAS RASopathy VCEP BS1 threshold of 0.025% and BA1 threshold of 0.05%.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts no significant splice impact for this intronic change, with a maximum delta score of 0.01, which does not support PP3 and leaves BP7 incomplete without the additional conservation evidence required by the VCEP rule.

spliceai ↗ cspec ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 3.98476e-05; MAF= 0.00398%, 11/276052 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000142491; MAF= 0.01425%, 1/7018 alleles, homozygotes = 0); grpmax FAF= 3.979e-05.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.000109975; MAF= 0.01100%, 175/1591272 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000135432; MAF= 0.01354%, 10/73838 alleles, homozygotes = 0); grpmax FAF= 0.00011553.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (2 clinical laboratories) and as Benign (1 clinical laboratory) and as Likely Benign by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
06
Cancer hotspots
No cancer hotspot summary recorded.