NIN p.Pro1900=
c.5700C>A · rs2041095554 · VCV2956465
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00178%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.079 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.74 | GERP 0.96, phastCons 0.14 |
| Overall | ||
| CADD | 6.733 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00178%
European (non-Finnish) · 21/1,179,954 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.0013%
21/1,614,012 alleles · very rare
exomes 21/1,461,790 · genomes 0/152,222 · 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
- NIN
- Protein
- p.Pro1900=
- Coding
- c.5700C>A
- MANE Select
- NM_020921
- dbSNP
- rs2041095554
- Type
- single nucleotide variant
- Location
- chr14:50738215 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
Similar variants
- NIN p.Pro1900Ala Uncertain significance ★ ⚠ same residue
- NIN p.Pro1900Leu Uncertain significance ★ ⚠ same residue
- NIN p.Arg2039Ter Likely pathogenic ★★ same type
- NIN p.Ala1049Thr Uncertain significance ★★ ⚠ same type
- NIN p.Ala1212Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1350Gly Uncertain significance ★★ ⚠ same type
- NIN p.Ala1741Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1755Thr 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/nin-p-pro1900 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown