NM_024408.3:c.6205C>A

NOTCH2 · NP_077719.2:p.(Pro2069Thr) · NM_024408.3

GRCh37: chr1:120459140 G>T · GRCh38: chr1:119916517 G>T

Gene: NOTCH2 Transcript: NM_024408.3

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

NOTCH2

Transcript

NM_024408.3

Protein

NP_077719.2:p.(Pro2069Thr)

gnomAD AF

6.200835128475103e-07 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

This variant is absent from ClinVar and has not been reported in the literature. No de novo, cosegregation, or functional data are available.

Multiple in silico tools predict a benign effect: REVEL score 0.225, BayesDel −0.234, and SpliceAI max delta 0.01.

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.

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.

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	This is a missense variant (c.6205C>A, p.Pro2069Thr) and does not fall into the default generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not met	No established pathogenic variant with the same amino acid change (Pro2069Thr or another alteration at Pro2069) has been identified in ClinVar or the literature. This variant is absent from ClinVar.	clinvar
PS2	Not met	No de novo evidence is available for this variant; no parental testing data or de novo reports were identified in ClinVar or the literature.	clinvar
PS3	Not met	No variant-specific functional studies were identified. In silico predictions (REVEL 0.225, BayesDel −0.234) are computational, not experimental functional data. OncoKB reports unknown oncogenic effect with no variant-specific functional evidence.	oncokb revel bayesdel
PS4	Not met	No case-control or prevalence data are available to assess enrichment of this variant in affected individuals versus controls.
PS5	Not met	No reputable source has reported this variant as pathogenic. The variant is absent from ClinVar and no literature reports a pathogenic classification.	clinvar
PM1	Not met	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. In the absence of domain-level guidance, PM1 cannot be applied.
PM2	Met	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 gnomad_v2 gnomad_canada
PM3	N/A	PM3 applies to recessive disorders; NOTCH2-associated conditions (Alagille syndrome, Hajdu-Cheney syndrome) are autosomal dominant.
PM4	N/A	PM4 applies to protein length changes (in-frame deletions/insertions, stop-loss); this is a single-nucleotide missense substitution.
PM5	Not met	No same-residue comparator pathogenic variants were identified. Automated PM5 candidate harvesting returned no results; ClinVar contains no variants at position 2069 with an alternate pathogenic missense change.	pm5_candidates clinvar
PM6	Not met	No de novo evidence is available for this variant; no confirmed de novo observations were identified in ClinVar or the literature.	clinvar
PP1	Not met	No cosegregation or family data are available for this variant.
PP2	Not assessed	Unable to assess missense constraint for NOTCH2. The HCI prior score is not available for this gene, and no gnomAD missense Z-score or constraint metrics were retrieved. Without these data, PP2 cannot be reliably applied.
PP3	Not met	Multiple lines of in silico evidence do not support a deleterious effect. REVEL score is 0.225 (well below the 0.5 pathogenic threshold), BayesDel is −0.234 (negative/benign range), and SpliceAI predicts no splicing impact (max delta 0.01). All available computational predictions point toward a benign effect.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or clinical data were provided to assess whether the clinical presentation is highly specific for a NOTCH2-related disorder.
PP5	Not met	This variant is absent from ClinVar; no reputable source has reported a pathogenic classification.	clinvar
BA1	Not met	The gnomAD v4.1 allele frequency is 6.2×10⁻⁷, well below the 1% BA1 threshold for a dominant disorder. The variant is absent from gnomAD v2.1.	gnomad_v4 gnomad_v2
BS1	Not met	The gnomAD v4.1 allele frequency is 6.2×10⁻⁷, well below the 0.3% BS1 threshold. The variant is too rare to satisfy BS1.	gnomad_v4 gnomad_v2
BS2	Not met	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. NOTCH2-related disorders (Alagille syndrome, Hajdu-Cheney syndrome) may show variable expressivity and reduced penetrance; a single population observation does not exclude pathogenicity.	gnomad_v4
BS3	Not met	No well-established functional studies demonstrate a neutral effect for this variant. In silico predictions (REVEL, BayesDel) are computational tools and do not constitute BS3-level experimental functional evidence. OncoKB reports no variant-specific functional data.	oncokb revel bayesdel
BS4	Not met	No segregation data are available to assess lack of cosegregation with disease in affected family members.
BP1	Not met	BP1 applies when a missense variant occurs in a gene for which primarily truncating variants cause disease. NOTCH2 is associated with both Alagille syndrome (caused by missense and truncating JAG1/NOTCH2 variants) and Hajdu-Cheney syndrome (caused by truncating variants in exon 34). Since the disease spectrum includes pathogenic missense variants, BP1 does not apply.	pvs1_gene_context
BP2	Not met	No data are available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. This variant is a single-nucleotide missense substitution.
BP4	Met	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 bayesdel spliceai
BP5	Not met	No alternate molecular basis for disease has been identified in a case carrying this variant.
BP6	Not met	This variant is absent from ClinVar; no reputable source has reported a benign classification.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splice impact and low conservation. This is a missense variant (c.6205C>A, p.Pro2069Thr), not a synonymous variant.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.