NM_024408.3:c.782T>G (p.Ile261Ser) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles), meeting PM2 at supporting strength.1 This variant has been reported in ClinVar (Variation ID 591665) as Uncertain significance by a single clinical testing laboratory (Labcorp Genetics, criteria provided, single submitter); no submitter has classified it as pathogenic or benign.2 No published functional studies, de novo observations, case-control enrichment, or family segregation data exist for this specific variant.3 In silico predictions are discordant: REVEL (0.80) supports a deleterious effect while BayesDel (0.402) does not; SpliceAI predicts no splicing impact (max delta 0.02). Neither PP3 nor BP4 can be applied.4 PVS1 is not applicable as this is a missense variant outside the null-variant buckets defined by ClinGen SVI PVS1 recommendations (PMC6185798).5 The only applicable criterion is PM2 (supporting); one supporting pathogenic criterion is insufficient to classify this variant above Variant of Uncertain Significance per ACMG/AMP 2015 combination rules.6
NOTCH2
Final classification
VUS
NOTCH2 c.782T>G · p.Ile261Ser
NOTCH2
NM_024408.3:c.782T>G (p.Ile261Ser) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (0 alleles), meeting PM2 at supporting strength.
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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2
VUS
NOTCH2 c.782T>G
PM2
→
VUS
3
oncokb ↗
4
revelbayesdelspliceai ↗
5
pvs1_generic_framework ↗pvs1_variant_assessment
6
generic_acmg_combination_rules
Gene diagram
· NM_024408.3 · variants mapped to exon structure
NOTCH2
NM_024408.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 21 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
NM_024408.3:c.782T>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (0 alleles across all population databases). The allele frequency (0) is below the PM2 threshold of <0.1% for a rare variant in a dominant disorder gene.
gnomAD v2.1: 0 alleles (absent)gnomAD v4.1: 0 alleles (absent)gnomAD-Canada v1.0: 0 alleles (absent)
Assessed · not applied
Pathogenic
PS1
No pathogenic variant with the same amino acid change (Ile261Ser) has been established in NOTCH2.
PS2
No de novo occurrence confirmed by both maternity and paternity testing has been reported.
PS3
No well-established in vitro or in vivo functional studies have been performed specifically on the I261S substitution.
PS4
PS4 requires statistically significant enrichment of the variant in affected individuals compared with controls.
PM1
Residue Ile261 lies within an EGF-like repeat domain (exon 5 of NOTCH2), which is critical for ligand binding and where pathogenic missense variants have been reported in Alagille syndrome.
PM5
No pathogenic missense variant at the same amino acid residue (Ile261) with a different amino acid change has been identified.
PM6
No de novo event (without confirmed maternity/paternity) has been reported.
PP1
No co-segregation data with disease in multiple affected family members is available.
PP2
While missense variants in NOTCH2 are a known disease mechanism (Alagille syndrome type 2, Hajdu-Cheney syndrome), gene-level missense constraint metrics (e.g., gnomAD missense Z-score, observed/expected ratio) have not been evaluated to confirm a low rate of benign missense variation in NOTCH2, which is required for PP2 application per ACMG/AMP 2015 guidelines.
PP3
In silico predictions are discordant.
PP4
No patient phenotype or family history data are available for this case.
PP5
This variant is classified as Uncertain significance in ClinVar (Variation ID 591665) by a single clinical submitter (Labcorp Genetics, criteria provided, single submitter).
Benign
BA1
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0).
BS1
The variant is absent from all population databases (allele frequency = 0).
BS2
No observations of this variant in healthy adult controls at significant frequency have been reported.
BS3
No well-established in vitro or in vivo functional studies have demonstrated no damaging effect for the I261S substitution.
BS4
No evidence of non-segregation with disease in affected families is available.
BP2
No observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder has been reported.
BP4
In silico predictions are discordant.
BP5
No observation of this variant in a case with an alternate molecular basis for disease has been reported.
BP6
No reputable source has reported this variant as benign.
N/A · 3
PVS1 · BP1 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
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.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 591665)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.8. BayesDel score = 0.401803.
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
Triaged references · 2 PMIDs not cited in assessment
25741868 ↗
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR