NM_000435.2:c.2299C>A (p.Arg767Ser) is a missense variant in NOTCH3 with extremely low population frequency (1/1,475,078 alleles in gnomAD v4.1, AF = 6.78e-7), meeting PM2 at supporting level.1 Multiple in silico predictors (REVEL 0.073, BayesDel −0.352, SpliceAI max delta 0.10) concordantly predict a benign effect, satisfying BP4 at supporting level.2 The variant is absent from ClinVar, COSMIC, and the published literature. No functional studies, segregation data, de novo reports, or same-residue pathogenic comparators are available.3 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced and insufficient to classify this variant as either likely pathogenic or likely benign per generic ACMG/AMP 2015 combination rules (PMID:25741868). The variant is classified as a Variant of Uncertain Significance (VUS).4
NOTCH3
Final classification
VUS
NOTCH3 c.2299C>A · p.Arg767Ser
NOTCH3
NM_000435.2:c.2299C>A (p.Arg767Ser) is a missense variant in NOTCH3 with extremely low population frequency (1/1,475,078 alleles in gnomAD v4.1, AF = 6.78e-7), meeting PM2 at supporting level.
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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2
BP4
VUS
NOTCH3 c.2299C>A
PM2 + BP4
→
VUS
2
revelbayesdelspliceai ↗
4
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
NM_000435.2:c.2299C>A is extremely rare in population databases. The variant is present at a single allele in gnomAD v4.1 (AF = 6.78 × 10⁻⁷; 1/1,475,078 alleles, 0 homozygotes), with its highest subpopulation frequency in European (non-Finnish) at 9.19 × 10⁻⁷ (1/1,088,162). It is absent from gnomAD v2.1 and gnomAD-Canada. This frequency is well below the 0.1% (0.001) PM2 threshold for non-VCEP adjudication.
gnomAD v4.1: 1/1475078 alleles
✓
BP4
supporting
Benign
Multiple independent in silico tools predict a benign effect for NM_000435.2:c.2299C>A (p.Arg767Ser). REVEL score is 0.073 (well below pathogenic threshold), BayesDel score is −0.352 (negative, consistent with benign), and SpliceAI predicts no splice-altering effect (max delta = 0.10). Three concordant benign predictions from independent algorithms satisfy BP4 at supporting benign level.
REVEL: 0.073 (benign-leaningbelow 0.5 threshold)BayesDel: -0.352 (negative
Assessed · not applied
Pathogenic
PS1
No alternative nucleotide change at NOTCH3 c.2299 has been reported as pathogenic in ClinVar or the literature.
PS2
No de novo observation with confirmed maternity and paternity has been reported for NM_000435.2:c.2299C>A.
PS3
No functional or experimental studies testing NM_000435.2:c.2299C>A (p.Arg767Ser) were identified.
PS4
No case-control studies demonstrating statistically higher prevalence of NM_000435.2:c.2299C>A in affected individuals compared to controls are available.
PM1
Residue Arg767 is not located in a statistically significant mutational hotspot per cancerhotspots.org.
PM5
No pathogenic missense variant at the same amino acid residue (Arg767) has been identified in ClinVar.
PM6
No de novo observation (maternity and paternity unconfirmed) has been reported for NM_000435.2:c.2299C>A.
PP1
No cosegregation data with disease in multiple affected family members is available for NM_000435.2:c.2299C>A.
PP2
PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common disease mechanism.
PP3
Multiple in silico tools predict a benign effect for NM_000435.2:c.2299C>A (p.Arg767Ser).
PP4
No detailed patient phenotype or family history data are available to assess whether the phenotype is highly specific for NOTCH3-related disease.
PP5
NM_000435.2:c.2299C>A is absent from ClinVar and has not been reported as pathogenic by any reputable clinical diagnostic laboratory or expert panel.
Benign
BA1
The allele frequency in gnomAD v4.1 is 6.78 × 10⁻⁷ (0.00007%), far below the 1% BA1 threshold.
BS1
The allele frequency in gnomAD v4.1 (AF = 6.78 × 10⁻⁷, highest in NFE at 9.19 × 10⁻⁷) is far below the 0.3% non-VCEP BS1 threshold.
BS2
While a single allele is observed in gnomAD v4.1, there is no confirmatory evidence that this carrier is an unaffected healthy adult, and a single observation is insufficient to meet BS2 requirements for a dominant disorder.
BS3
No functional or experimental studies demonstrating that NM_000435.2:c.2299C>A (p.Arg767Ser) has no damaging effect on protein function or splicing have been identified.
BS4
No family studies demonstrating lack of segregation of NM_000435.2:c.2299C>A with disease are available.
BP1
BP1 applies when a missense variant is found in a gene where only truncating variants cause disease.
BP2
No data are available to determine whether NM_000435.2:c.2299C>A has been observed in trans with a known pathogenic NOTCH3 variant in a case of recessive disease.
BP5
No data are available demonstrating that NM_000435.2:c.2299C>A is found in a case with an alternate established molecular basis for disease.
BP6
NM_000435.2:c.2299C>A is absent from ClinVar and has not been reported as benign by any reputable clinical diagnostic laboratory or expert panel.
N/A · 5
PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.7793e-07; MAF= 0.00007%, 1/1475078 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.18981e-07; MAF= 0.00009%, 1/1088162 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
6.8e-05%
· 1 / 1,475,078
0 hom
0 hom
European (non-Finnish) 1 / 1,088,162 |
9.2e-05% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.073. BayesDel score = -0.351535.
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.
COSMIC
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