NIN p.Ser748=
c.2244C>T · rs200278498 · VCV211601
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.38%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.003 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.22 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.97 | GERP -1.1 |
| Overall | ||
| CADD | 2.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.38%
South Asian · 3,077/91,080 alleles
Filtering AF
3.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.24%
Overall
0.206%
3,330/1,614,124 alleles · low-frequency
exomes 3,156/1,461,890 · genomes 174/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.38% | 30 |
| Remaining individualsnot grpmax-eligible | 0.278% | 359 |
| Middle Eastern | 0.115% | 866 |
| East Asian | 0.0156% | 6,411 |
| African / African-American | 0.008% | 12,499 |
| European (non-Finnish) | 0.00483% | 20,702 |
| Admixed American | 0.00333% | 30,014 |
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.Ser748=
- Coding
- c.2244C>T
- MANE Select
- NM_020921
- dbSNP
- rs200278498
- Type
- single nucleotide variant
- Location
- chr14:50760012 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
Similar variants
- 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
- NIN p.Ala1755Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1813Gly 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-ser748 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown