NM_000435.2:c.5946G>T

NOTCH3 · NP_000426.2:p.(Glu1982Asp) · NM_000435.2

GRCh37: chr19:15272493 C>A · GRCh38: chr19:15161682 C>A

Gene: NOTCH3 Transcript: NM_000435.2

Final call

VUS

PM2 moderate BP4 supporting benign

Variant details

Gene

NOTCH3

Transcript

NM_000435.2

Protein

NP_000426.2:p.(Glu1982Asp)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000435.2:c.5946G>T (p.Glu1982Asp) is a missense variant in NOTCH3 exon 33 that is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2 at moderate strength.

Multiple computational predictors (REVEL 0.282, BayesDel -0.291, SpliceAI max delta 0.03) uniformly support a benign effect, meeting BP4 at supporting benign strength.

No other ACMG/AMP criteria are met. The variant is absent from ClinVar, has no reported functional data, and is not located in a known mutational hotspot or critical functional domain. Evidence is insufficient for any classification beyond Variant of Uncertain Significance.

Applying generic ACMG/AMP 2015 combination rules: one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are in conflict. Neither the pathogenic nor benign evidence thresholds are reached, resulting in a classification of Uncertain Significance.

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	NM_000435.2:c.5946G>T is a missense variant (p.Glu1982Asp). PVS1 applies only to null variants — nonsense, frameshift, canonical ±1,2 splice consensus, initiation codon, or exon-level deletions. This variant does not fall into any of those categories and therefore does not trigger PVS1 assessment under the ClinGen SVI PVS1 framework (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No same amino acid change (p.Glu1982Asp) has been previously reported as pathogenic in ClinVar or the literature. PS1 requires a previously established pathogenic variant at the same amino acid position with the same change.	clinvar
PS2	Not met	No de novo observation with confirmed paternity and maternity has been reported for NM_000435.2:c.5946G>T in any literature source.
PS3	Not met	No well-established in vitro or in vivo functional studies have been performed on NM_000435.2:c.5946G>T (p.Glu1982Asp). OncoKB reports unknown oncogenic effect with no variant-specific curated functional data. No publications identified with functional assay data for this variant.	oncokb
PS4	Not met	No case-control or cohort prevalence data are available for NM_000435.2:c.5946G>T. The variant has not been reported in affected individuals in any literature source.
PS5	Not met	No association study or reputable source has established NM_000435.2:c.5946G>T as disease-associated. No CSPEC/VCEP for NOTCH3 exists to provide gene-level guidance.
PM1	Not met	NM_000435.2:c.5946G>T (p.Glu1982Asp) does not lie in a statistically significant mutational hotspot per cancerhotspots.org. While NOTCH3 position 1982 resides in the intracellular domain (exon 33), no literature evidence supports this specific residue as a critical functional domain for germline disease. CADASIL-associated pathogenic variants cluster in EGF-like repeats in the extracellular domain, not in the C-terminal intracellular region.
PM2	Met	NM_000435.2:c.5946G>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Population frequency is 0%, well below the 0.1% PM2 threshold for a rare missense variant in a gene associated with autosomal dominant disease.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No same-residue comparator variant at p.Glu1982 with a different amino acid change has been classified as pathogenic in ClinVar. Automated PM5 candidate search returned zero candidates.	pm5_candidates clinvar
PM6	Not met	No de novo observation (without confirmed paternity and maternity) has been reported for NM_000435.2:c.5946G>T in any literature source.
PP1	Not met	No co-segregation data are available for NM_000435.2:c.5946G>T. No family studies have been reported.
PP2	Not met	PP2 requires a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease. NOTCH3 CADASIL is caused by cysteine-altering missense variants in EGF-like repeats. This variant (p.Glu1982Asp, exon 33) is not a cysteine-altering substitution and lies in the intracellular domain, outside the EGF-repeat region where pathogenic missense variants cluster. PP2 cannot be applied without CSPEC/VCEP guidance and specific gene-level missense constraint metrics.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. REVEL score is 0.282 (below the 0.5 pathogenic threshold), BayesDel score is -0.291 (negative direction, consistent with benign), and SpliceAI predicts no significant splice impact (max delta score 0.03). All in silico tools point toward a benign or neutral effect rather than a deleterious one.	revel bayesdel spliceai
PP4	Not met	No patient-specific phenotype or family history information is available for this case. PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.
PP5	Not met	NM_000435.2:c.5946G>T is absent from ClinVar. No reputable source, including expert panels or clinical laboratories, has classified this variant as pathogenic.	clinvar
BA1	Not met	NM_000435.2:c.5946G>T is absent from all population databases (gnomAD v2.1, v4.1, and gnomAD-Canada). The allele frequency is 0%, far below the 1% BA1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	Population frequency is 0% in gnomAD, below the 0.3% BS1 threshold. The variant is too rare in population databases to meet BS1.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	NM_000435.2:c.5946G>T has not been observed in any healthy adult individual in gnomAD or the literature. No data support observation in a healthy individual at an age when disease would be fully penetrant.
BS3	Not met	No well-established in vitro or in vivo functional studies have demonstrated no damaging effect for NM_000435.2:c.5946G>T. No functional data exist for this variant.
BS4	Not met	No non-segregation data are available for NM_000435.2:c.5946G>T. No family studies have been reported.
BP1	Not met	BP1 applies when a missense variant occurs in a gene where primarily truncating variants are known to cause disease. NOTCH3 CADASIL is primarily caused by cysteine-altering missense variants, not truncating variants. While NOTCH3 loss-of-function has been reported as a disease modifier in some studies, the predominant established mechanism for CADASIL is missense-mediated. BP1 is not applicable.
BP2	Not met	No observation of NM_000435.2:c.5946G>T in trans with a known pathogenic dominant variant in NOTCH3 has been reported.
BP4	Met	Multiple lines of computational evidence suggest no deleterious impact on the gene or gene product. REVEL score is 0.282 (below the typical pathogenic threshold of 0.5), BayesDel score is -0.291 (negative direction, consistent with benign), and SpliceAI predicts no splice alteration (max delta score 0.03). Three independent in silico algorithms using different methodologies all support a benign interpretation.	revel bayesdel spliceai
BP5	Not met	NM_000435.2:c.5946G>T has not been observed in a case where an alternative molecular basis for disease was identified. No such case has been reported.
BP6	Not met	NM_000435.2:c.5946G>T is absent from ClinVar. No reputable source, including expert panels or clinical laboratories, has classified this variant as benign.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splice impact. NM_000435.2:c.5946G>T is a missense variant (p.Glu1982Asp) and does not meet BP7 criteria.

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