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NOTCH3
Final classification
VUS
NOTCH3 c.3452G>A · p.Gly1151Glu
NOTCH3

NM_000435.2:c.3452G>A (p.Gly1151Glu) is a missense variant in NOTCH3, a gene in which missense variants are a well-established cause of CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy).

Gene
NOTCH3
Transcript
NM_000435.2
HGVS · transcript:coding
NM_000435.2:c.3452G>A
Consequence
N/A
GRCh38
chr19:15179372 C>T
GRCh37
chr19:15290183 C>T
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: PM2 supporting, PP3 supporting; combination = 2 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
NOTCH3 c.3452G>A

NM_000435.2:c.3452G>A (p.Gly1151Glu) is a missense variant in NOTCH3, a gene in which missense variants are a well-established cause of CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy).1 This variant is ultra-rare in population databases, absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 1.24e-6 (2/1,614,098 alleles, 0 homozygotes), well below the 0.1% PM2 threshold (PM2_Supporting).2 In silico analysis with REVEL yields a score of 0.866, predicting a damaging effect on the protein. BayesDel is borderline at 0.474, and SpliceAI predicts no splice impact (max delta 0.02) (PP3_Supporting).3 No variant-specific functional data, de novo observations, case-control studies, segregation data, or ClinVar classifications are available for this variant. The variant is absent from ClinVar and has not been reported in COSMIC or literature.4 With only two supporting-level pathogenic criteria (PM2_Supporting, PP3_Supporting) and no benign criteria met, the evidence is insufficient to classify this variant as pathogenic, likely pathogenic, benign, or likely benign under the ACMG/AMP 2015 framework. This variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + PP3 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000435.2 · variants mapped to exon structure
NOTCH3 NM_000435.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 and present in gnomAD v4.1 at an ultra-rare allele frequency of 1.24e-6 (2/1,614,098 alleles, 0 homozygotes), well below the 0.1% PM2 threshold for non-VCEP adjudication.
gnomAD v2.1: absent. gnomAD v4.1: AF=1.24e-6 (2/1614098 alleles
PP3 supporting Pathogenic
REVEL predicts a damaging effect with a score of 0.866 (above the 0.5 threshold). BayesDel score of 0.474 is borderline. SpliceAI reports no significant splice impact (max delta 0.02). At least one in silico predictor (REVEL) supports a deleterious effect on the gene product, meeting supporting-level PP3.
REVEL: 0.866 (damaging). BayesDel: 0.474 (borderlinebelow 0.5). SpliceAI: max delta 0.02 (no splice impact).
Assessed · not applied
Pathogenic
PS1 No prior pathogenic variant resulting in the same amino acid change (p.Gly1151Glu) has been reported in ClinVar or the literature.
PS2 No de novo observation with confirmed paternity and maternity has been reported for this variant.
PS3 No variant-specific functional data are available for p.Gly1151Glu.
PS4 No case-control studies or prevalence data in affected individuals versus controls are available for this variant.
PM1 Residue G1151 is not located within a statistically significant mutational hotspot as determined by cancerhotspots.org.
PM5 No same-residue comparator variant (different missense change at p.Gly1151) with an established pathogenic classification was identified.
PM6 No de novo observation (without confirmation of paternity and maternity) has been reported for this variant.
PP1 No co-segregation data with disease in multiple affected family members are available for this variant.
PP2 PP2 requires demonstration that the gene has a low rate of benign missense variation (typically via a high missense Z-score) in a gene where missense variants are a common mechanism of disease.
PP4 No patient phenotype or clinical data are available to assess whether the phenotype is highly specific for NOTCH3-related disease.
PP5 This variant is absent from ClinVar.
Benign
BA1 The allele frequency in gnomAD v4.1 is 1.24e-6 (0.000124%), far below the 1% BA1 threshold.
BS1 The allele frequency in gnomAD v4.1 is 1.24e-6, far below the 0.3% BS1 threshold for non-VCEP adjudication.
BS2 No evidence that this variant has been observed in healthy adults at an age when full penetrance of NOTCH3-related disease would be expected.
BS3 No well-established functional studies demonstrating no damaging effect on protein function or splicing are available for this variant.
BS4 No segregation data in affected families are available to demonstrate lack of co-segregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease.
BP2 No observation of this variant in trans with a known pathogenic variant in a gene associated with a fully penetrant dominant disorder has been reported.
BP4 REVEL predicts a damaging effect with a score of 0.866, contradicting benign in silico predictions.
BP5 No case has been reported where an alternative molecular basis for disease was identified in an individual carrying this variant, which would suggest the variant is not causative.
BP6 This variant is absent from ClinVar.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.23908e-06; MAF= 0.00012%, 2/1614098 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.5998e-05; MAF= 0.00160%, 1/62508 alleles, homozygotes = 0).
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
0.00012% · 2 / 1,614,098
0 hom
Remaining individuals
1 / 62,508
0.0016%
European (non-Finnish)
1 / 1,180,042
8.5e-05%
+ 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.866. BayesDel score = 0.47403.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. NOTCH3 encodes a Type I transmembrane protein of the Notch family. Missense and nonsense mutations in NOTCH3 have been identified in various cancers.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots