NEB p.Pro4790=
c.14370G>A · rs747837704 · VCV932372
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.233%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.7 |
| Overall | ||
| CADD | 4.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.233%
European (non-Finnish) · 1,327/568,596 alleles
Filtering AF
0.223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.219%
Overall
0.179%
1,492/835,378 alleles · rare
exomes 1,358/746,642 · genomes 134/88,736 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.233% | 428 |
| Remaining individualsnot grpmax-eligible | 0.17% | 589 |
| Ashkenazi Jewishnot grpmax-eligible | 0.161% | 620 |
| Middle Eastern | 0.108% | 924 |
| African / African-American | 0.0821% | 1,218 |
| Finnishnot grpmax-eligible | 0.064% | 1,562 |
| Admixed American | 0.00948% | 10,552 |
| East Asian | 0.00282% | 35,502 |
| South Asian | 0.00176% | 56,776 |
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
- NEB
- Protein
- p.Pro4790=
- Coding
- c.14370G>A
- MANE Select
- NM_001164508
- dbSNP
- rs747837704
- Type
- single nucleotide variant
- Location
- chr2:151594154 (GRCh38)
- Gene constraint
- LOEUF 0.597 · pLI <0.01 (gnomAD)
- Residue 4790
- a UniProt-annotated variant site (in amc6)
Similar variants
- NEB c.11910+1G>A Likely pathogenic ★★★ same type
- NEB c.6076-1G>T Likely pathogenic ★★★ same type
- NEB c.78+1G>A Pathogenic ★★★ same type
- NEB p.Arg2313Ter Pathogenic ★★★ same type
- NEB p.Asp498Gly Likely pathogenic ★★★ ⚠ same type
- NEB p.Ser6366Ile Pathogenic ★★★ same type
- NEB p.Ser6648= Pathogenic ★★★ same type
- NEB c.22590+2T>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/neb-p-pro4790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown