NM_024408.3:c.6205C>A (p.Pro2069Thr) is a missense variant in exon 34 of NOTCH2. It is present at extremely low frequency in gnomAD v4.1 (1/1,612,686 alleles; AF=6.2×10⁻⁷) and absent from gnomAD v2.1 and gnomAD-Canada.1 This variant is absent from ClinVar and has not been reported in the literature. No de novo, cosegregation, or functional data are available.2 Multiple in silico tools predict a benign effect: REVEL score 0.225, BayesDel −0.234, and SpliceAI max delta 0.01.3 PM2 (supporting) is met due to extreme rarity in population databases. BP4 (supporting) is met based on concordant benign in silico predictions. No other criteria are met.4 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is conflicting and insufficient to classify this variant as either likely pathogenic or likely benign. The variant is classified as a Variant of Uncertain Significance (VUS) per the generic ACMG/AMP 2015 framework.5
NOTCH2
Final classification
VUS
NOTCH2 c.6205C>A · p.Pro2069Thr
NOTCH2
NM_024408.3:c.6205C>A (p.Pro2069Thr) is a missense variant in exon 34 of NOTCH2. It is present at extremely low frequency in gnomAD v4.1 (1/1,612,686 alleles; AF=6.2×10⁻⁷) and absent from gnomAD v2.1 and gnomAD-Canada.
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; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2
BP4
VUS
NOTCH2 c.6205C>A
PM2 + BP4
→
VUS
Gene diagram
· NM_024408.3 · variants mapped to exon structure
NOTCH2
NM_024408.3
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 present at extremely low frequency in gnomAD v4.1 (AF=6.2×10⁻⁷; 1/1,612,686 alleles, no homozygotes) and is absent from gnomAD v2.1 and gnomAD-Canada. The allele frequency is well below the 0.1% threshold for a dominant disorder.
gnomAD v4.1: 1/1612686 alleles (AF=6.20e-07)
✓
BP4
supporting
Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.225 (below 0.5 pathogenic threshold), BayesDel is −0.234 (negative, in the benign range), and SpliceAI predicts no splicing impact (max delta 0.01). Three independent in silico tools consistently predict a benign effect.
REVEL: 0.225 (benign). BayesDel: -0.234284 (benign). SpliceAI: max delta 0.01 (no splicing impact). Three concordant benign in silico predictions.
Assessed · not applied
Pathogenic
PS1
No established pathogenic variant with the same amino acid change (Pro2069Thr or another alteration at Pro2069) has been identified in ClinVar or the literature.
PS2
No de novo evidence is available for this variant; no parental testing data or de novo reports were identified in ClinVar or the literature.
PS3
No variant-specific functional studies were identified.
PS4
No case-control or prevalence data are available to assess enrichment of this variant in affected individuals versus controls.
PM1
Although position 2069 lies within the NOTCH2 intracellular domain near the ankyrin repeat region, the variant is not in a statistically significant mutational hotspot (cancerhotspots.org negative), and no CSPEC/VCEP domain-level specification for NOTCH2 PM1 application has been established.
PM5
No same-residue comparator pathogenic variants were identified.
PM6
No de novo evidence is available for this variant; no confirmed de novo observations were identified in ClinVar or the literature.
PP1
No cosegregation or family data are available for this variant.
PP2
Unable to assess missense constraint for NOTCH2.
PP3
Multiple lines of in silico evidence do not support a deleterious effect.
PP4
No patient phenotype or clinical data were provided to assess whether the clinical presentation is highly specific for a NOTCH2-related disorder.
PP5
This variant is absent from ClinVar; no reputable source has reported a pathogenic classification.
Benign
BA1
The gnomAD v4.1 allele frequency is 6.2×10⁻⁷, well below the 1% BA1 threshold for a dominant disorder.
BS1
The gnomAD v4.1 allele frequency is 6.2×10⁻⁷, well below the 0.3% BS1 threshold.
BS2
A single heterozygous observation in gnomAD v4.1 (NFE male) is insufficient to establish that the variant is benign when observed in a healthy adult.
BS3
No well-established functional studies demonstrate a neutral effect for this variant.
BS4
No segregation data are available to assess lack of cosegregation with disease in affected family members.
BP1
BP1 applies when a missense variant occurs in a gene for which primarily truncating variants cause disease.
BP2
No data are available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP5
No alternate molecular basis for disease has been identified in a case carrying this variant.
BP6
This variant is absent from ClinVar; no reputable source has reported a benign classification.
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= 6.20084e-07; MAF= 0.00006%, 1/1612686 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.48371e-07; MAF= 0.00008%, 1/1178730 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
6.2e-05%
· 1 / 1,612,686
0 hom
0 hom
European (non-Finnish) 1 / 1,178,730 |
8.5e-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 = 0.01). REVEL score = 0.225. BayesDel score = -0.234284.
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. NOTCH2 encodes a transmembrane receptor that regulates many aspects of development by affecting cell-fate determination.
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