NF1 p.Pro1840=
c.5520C>A · rs786201638 · VCV184716
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
2
hereditary neoplastic syndrome
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 -0.3 | GERP -0.86, phastCons 0.1 |
| Overall | ||
| CADD | 7.174 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,996 alleles
Overall
6.2e-05%
1/1,613,978 alleles · very rare
exomes 0/1,461,838 · genomes 1/152,140 · joint denominator
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
- NF1
- Protein
- p.Pro1840=
- Coding
- c.5520C>A
- MANE Select
- NM_001042492
- dbSNP
- rs786201638
- Type
- single nucleotide variant
- Location
- chr17:31327750 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- NF1 p.Pro1840Thr Uncertain significance ★★ same residue
- NF1 p.Pro1840Arg Uncertain significance ★ ⚠ same residue
- NF1 p.Pro1840Ser Uncertain significance ★ same residue
- NF1 p.Pro1840fs Pathogenic ★ same residue
- NF1 c.1062+1G>A Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1062+1G>C Pathogenic ★★ same condition
- NF1 c.1062+2T>A Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1062+2T>C Pathogenic/Likely pathogenic ★★ same condition
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/nf1-p-pro1840 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown