NOTCH2 p.Ser104=
c.312A>G · rs2793999 · VCV1174709
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | |
| Overall | ||
| CADD | 0.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
South Asian · 30/91,014 alleles
Filtering AF
0.0237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0205%
Overall
0.00855%
138/1,613,378 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.033% | 3,034 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| Admixed American | 0.01% | 10,002 |
| European (non-Finnish) | 0.0078% | 12,819 |
| East Asian | 0.00446% | 22,440 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NOTCH2
- Protein
- p.Ser104=
- Coding
- c.312A>G
- MANE Select
- NM_024408
- dbSNP
- rs2793999
- Type
- single nucleotide variant
- Location
- chr1:120005432 (GRCh38)
- Gene constraint
- LOEUF 0.151 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.51 · 2 PDB
Similar variants
- NOTCH2 p.Arg2003Ter Pathogenic/Likely pathogenic ★★ same type
- NOTCH2 p.Arg2400Ter Pathogenic ★★ same type
- NOTCH2 p.Gln2223Ter Pathogenic ★★ same type
- NOTCH2 p.Gln2263Ter Pathogenic ★★ same type
- NOTCH2 p.Gln2285Ter Pathogenic/Likely pathogenic ★★ same type
- NOTCH2 c.2753-8T>A Uncertain significance ★★ same type
- NOTCH2 c.5214-10A>G Uncertain significance ★★ same type
- NOTCH2 c.874+4T>C Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/notch2-p-ser104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown