NF1 p.Val153=
c.459C>T · rs2143673716 · VCV1741767
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
2
Cardiovascular phenotype
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 0.97 | GERP -0.45, phastCons 1 |
| Overall | ||
| CADD | 8.379 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,972 alleles
Overall
6.2e-05%
1/1,614,088 alleles · very rare
exomes 1/1,461,802 · genomes 0/152,286 · 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.Val153=
- Coding
- c.459C>T
- MANE Select
- NM_001042492
- dbSNP
- rs2143673716
- Type
- single nucleotide variant
- Location
- chr17:31163356 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 153
- an α-helix
Similar variants
- NF1 p.Val153Asp Uncertain significance ★★ ⚠ same residue
- NF1 p.Val153Ile Uncertain significance ★★ same residue
- NF1 p.Val153_Phe154insTer Pathogenic ★★ same residue
- NF1 p.Val153Ala Uncertain significance ★ ⚠ same residue
- NF1 c.1062+2T>C Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1062+3A>G Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1063-13G>A Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1063-1G>A 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-val153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown