NM_017617.5:c.1093C>T

NOTCH1 · NP_060087.3:p.(Arg365Cys) · NM_017617.5

GRCh37: chr9:139413049 G>A · GRCh38: chr9:136518597 G>A

Gene: NOTCH1 Transcript: NM_017617.5

Final call

VUS

PM1 supporting PM2 moderate

Variant details

Gene

NOTCH1

Transcript

NM_017617.5

Protein

NP_060087.3:p.(Arg365Cys)

gnomAD AF

ClinVar

Likely pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

Residue Arg365 is located in a statistically significant mutational hotspot per cancerhotspots.org, meeting PM1 at supporting strength.

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.

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.

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.

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).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is a missense variant (p.Arg365Cys) that does not fall into the default generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. The ClinGen SVI PVS1 generic framework (PMC6185798) is not applicable to this variant class.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No known pathogenic variant with a different amino acid change at residue Arg365 was identified. PM5 candidate search returned no same-residue comparator variants in ClinVar.	pm5_candidates clinvar
PS2	Not met	No de novo data are available for this variant. Neither ClinVar submissions nor the literature packet contain de novo observations.	clinvar
PS3	Not met	No variant-specific functional data are available for NM_017617.5:c.1093C>T. OncoKB curates this variant as Likely Oncogenic with variant-specific literature references, but the underlying primary publications are not available in full text for independent verification. The 21 somatic occurrences in COSMIC indicate recurrence in cancer but do not constitute experimental functional characterization. No publications in the case folder directly tested p.Arg365Cys in a functional assay.	oncokb
PS4	Not met	No case-control or case series data are available establishing an association between this variant and disease. The variant is absent from gnomAD, precluding case-control comparison. ClinVar submissions do not include phenotype details beyond 'Not Provided.'	clinvar gnomad_v2 gnomad_v4
PS5	Not met	PS5 is not applicable without family-based evidence establishing segregation or inheritance patterns. No family studies are available for this variant.
PM1	Met	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.	oncokb
PM2	Met	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).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue comparator variants with a different pathogenic missense change were identified in ClinVar. PM5 candidate harvesting returned zero candidates at residue Arg365.	pm5_candidates
PM6	Not met	No de novo data are available for this variant. PM6 requires confirmed de novo occurrence with maternity and paternity confirmation.	clinvar
PP1	Not met	No segregation data are available for this variant. PP1 requires cosegregation with disease in multiple affected family members.
PP2	N/A	PP2 requires a gene-specific threshold where missense variants are a recognized mechanism and the gene has a low rate of benign missense variation. No gene-specific PP2 framework is available for NOTCH1 under generic ACMG, and NOTCH1 disease is caused by both missense and truncating variants across the gene.	pvs1_gene_context
PP3	Not met	In silico predictions are conflicting and do not support a consistent deleterious effect. REVEL score is 0.62 (moderately elevated but below strong thresholds), while BayesDel score is 0.044 (suggesting benign). SpliceAI predicts no splicing impact (max delta score 0.00). The GeneDx ClinVar submission also notes that in silico analysis is inconsistent in its predictions. Conflicting computational evidence precludes application of PP3.	revel bayesdel spliceai
PP4	Not met	No detailed patient phenotype data are available for this variant. ClinVar submissions list 'Not Provided' or no condition labels, and no case reports with phenotypic descriptions were identified in the literature packet.	clinvar
PP5	Not met	ClinVar reports conflicting classifications: one submitter classifies as Likely Pathogenic (GeneDx, SCV000570514) and another as Uncertain Significance (Labcorp Genetics, SCV003459548). Both are single submitters without expert panel review. A split ClinVar classification does not meet PP5 criteria, which requires a consistent pathogenic call from a reputable source.	clinvar
BA1	Not met	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.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	This variant is absent from gnomAD across all queried datasets, with no allele frequency exceeding the BS1 threshold of >0.3% in any population.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data are available regarding observation of this variant in healthy adults. The variant is absent from gnomAD, precluding assessment of healthy carrier frequency.	gnomad_v2 gnomad_v4
BS3	Not met	No functional studies demonstrating no deleterious effect are available for this variant. BS3 requires well-established functional assays showing no damaging effect. No such data exist in the case folder.
BS4	Not met	No segregation data are available to demonstrate lack of cosegregation with disease. BS4 requires observation of non-segregation in affected family members.
BP1	N/A	BP1 applies when a missense variant occurs in a gene where only truncating variants are known to cause disease. NOTCH1 has both missense and truncating pathogenic variants reported in the germline literature (e.g., p.Glu756Ter, p.Cys575Ser, p.Tyr2209CysfsTer38), so BP1 does not apply.	pvs1_gene_context
BP2	Not met	No trans configuration data are available for this variant. BP2 requires observation of the variant in trans with a known pathogenic variant.
BP4	Not met	In silico predictions are conflicting and do not consistently suggest a benign effect. REVEL score is 0.62 (moderately elevated), while BayesDel score is 0.044 (low/benign direction) and SpliceAI predicts no impact. The discordance among predictors precludes application of BP4, which requires multiple lines of computational evidence consistently suggesting no impact.	revel bayesdel spliceai
BP5	Not met	No alternate molecular basis for disease has been identified in the available data. BP5 requires observation of a different pathogenic variant in a case with the same phenotype.
BP6	Not met	No reputable source has classified this variant as benign. ClinVar classifications are Likely pathogenic and Uncertain significance. BP6 requires a consistent benign classification from a reputable source.	clinvar
BP7	N/A	BP7 applies only to synonymous (silent) variants with no predicted splicing impact and non-conserved nucleotide. This is a missense variant (c.1093C>T, p.Arg365Cys) and does not qualify for BP7.
BP3	N/A	Skipped: variant is a substitution, not an in-frame indel.
PM3	N/A	Skipped: no trans configuration data available for recessive assessment.
PM4	N/A	Skipped: variant is a substitution, not an in-frame indel or stop-loss.

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