NRIP1 p.Ser798=
c.2394C>T · rs145934121 · VCV2053349
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.811%, eas)
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 -1.8 | GERP -4 |
| Overall | ||
| CADD | 4.541 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.811%
East Asian · 364/44,864 alleles
Filtering AF
0.743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.716%
Overall
0.0393%
635/1,613,900 alleles · rare
exomes 577/1,461,702 · genomes 58/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.811% | 123 |
| Finnishnot grpmax-eligible | 0.169% | 593 |
| Remaining individualsnot grpmax-eligible | 0.104% | 961 |
| South Asian | 0.0187% | 5,357 |
| Admixed American | 0.00834% | 11,997 |
| European (non-Finnish) | 0.00619% | 16,163 |
| African / African-American | 0.004% | 24,997 |
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
- NRIP1
- Protein
- p.Ser798=
- Coding
- c.2394C>T
- MANE Select
- NM_003489
- dbSNP
- rs145934121
- Type
- single nucleotide variant
- Location
- chr21:14965799 (GRCh38)
- Gene constraint
- LOEUF 0.489 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 46.10 · 17 PDB
- Residue 798
- the 'repression domain 3' region; the 'interaction with znf366' region
Similar variants
- NRIP1 p.Ala1096Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala360Ser Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala36Pro Uncertain significance ★★ ⚠ same type
- NRIP1 p.Ala792Val Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg1082Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg1122Gly Uncertain significance ★★ ⚠ same type
- NRIP1 p.Arg98Trp Uncertain significance ★★ ⚠ same type
- NRIP1 p.Asn45Asp 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/nrip1-p-ser798 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown