Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
NOTCH1
Final classification
VUS
NOTCH1 c.1093C>T · p.Arg365Cys
NOTCH1

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PM2 criterion at moderate strength for absence from population databases.

Gene
NOTCH1
Transcript
NM_017617.5
HGVS · transcript:coding
NM_017617.5:c.1093C>T
Consequence
N/A
GRCh38
chr9:136518597 G>A
GRCh37
chr9:139413049 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
NOTCH1 c.1093C>T

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PM2 criterion at moderate strength for absence from population databases.1 Residue Arg365 is located in a statistically significant mutational hotspot per cancerhotspots.org, meeting PM1 at supporting strength.2 In silico predictions are conflicting: REVEL score 0.62 suggests a moderately damaging effect while BayesDel score 0.044 suggests a benign effect and SpliceAI predicts no splicing impact (max delta 0.00). Neither PP3 nor BP4 can be applied due to discordant predictions.3 ClinVar reports conflicting classifications for this variant: Likely pathogenic (GeneDx, 1 submitter) and Uncertain significance (Labcorp Genetics, 1 submitter), both from single clinical laboratories without expert panel review. The split classification precludes application of PP5.4 No variant-specific functional data are available for NM_017617.5:c.1093C>T (p.Arg365Cys). OncoKB curates this variant as Likely Oncogenic based on somatic literature, but primary publications were not available in full text for independent verification. PS3 cannot be met without experimental functional characterization.5 Combined ACMG evidence: PM2 (moderate) and PM1 (supporting) are met. Per generic ACMG/AMP 2015 combination rules (PMID:25741868), one moderate and one supporting criterion does not reach the threshold for Likely Pathogenic (requires ≥2 moderate plus ≥2 supporting, or ≥3 moderate, or 1 moderate plus ≥4 supporting). The overall classification is Uncertain Significance (VUS).6

PM1 + PM2 VUS
3 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_017617.5 · variants mapped to exon structure
NOTCH1 NM_017617.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 supporting Pathogenic
Residue Arg365 is located in a statistically significant mutational hotspot as defined by cancerhotspots.org. This residue-level hotspot designation supports a functional role, although the exact variant (p.Arg365Cys) is not independently listed in the hotspot registry. PM1 is applied at supporting strength given the residue-level (rather than domain-level) hotspot evidence.
cancerhotspots.org identifies residue R365 as a statistically significant hotspot. The variant lies within the EGF-like repeat region of the NOTCH1 extracellular domain.
PM2 moderate Pathogenic
This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting the PM2 threshold for absence from population databases (allele frequency <0.1% and absent in all queried populations).
Absent from gnomAD v2.1 (AF=null)v4.1 (AF=null)and gnomAD-Canada v1.0 (AF=0.0
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant with a different amino acid change at residue Arg365 was identified.
PS2 No de novo data are available for this variant.
PS3 No variant-specific functional data are available for NM_017617.5:c.1093C>T.
PS4 No case-control or case series data are available establishing an association between this variant and disease.
PM6 No de novo data are available for this variant.
PP1 No segregation data are available for this variant.
PP3 In silico predictions are conflicting and do not support a consistent deleterious effect.
PP4 No detailed patient phenotype data are available for this variant.
PP5 ClinVar reports conflicting classifications: one submitter classifies as Likely Pathogenic (GeneDx, SCV000570514) and another as Uncertain Significance (Labcorp Genetics, SCV003459548).
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with no allele frequency data exceeding the BA1 threshold of >1% in any population.
BS1 This variant is absent from gnomAD across all queried datasets, with no allele frequency exceeding the BS1 threshold of >0.3% in any population.
BS2 No data are available regarding observation of this variant in healthy adults.
BS3 No functional studies demonstrating no deleterious effect are available for this variant.
BS4 No segregation data are available to demonstrate lack of cosegregation with disease.
BP2 No trans configuration data are available for this variant.
BP4 In silico predictions are conflicting and do not consistently suggest a benign effect.
BP5 No alternate molecular basis for disease has been identified in the available data.
BP6 No reputable source has classified this variant as benign.
N/A · 8 PVS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 Likely pathogenic (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 421340)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.62. BayesDel score = 0.0438125.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53025487, n = 21 times).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots