NIN p.Asp641=
c.1923C>T · rs538981711 · VCV2175750
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.41%, sas)
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 -0.17 | GERP -3.4, phastCons 0.003 |
| Overall | ||
| CADD | 1.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.41%
South Asian · 373/91,034 alleles
Filtering AF
0.375%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.362%
Overall
0.0277%
445/1,605,430 alleles · rare
exomes 414/1,453,652 · genomes 31/151,778 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.41% | 244 |
| Remaining individualsnot grpmax-eligible | 0.0689% | 1,452 |
| Middle Eastern | 0.0495% | 2,019 |
| East Asian | 0.00892% | 11,210 |
| Admixed American | 0.00667% | 14,989 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,590 |
| European (non-Finnish) | 0.00136% | 73,723 |
| African / African-American | 0.00134% | 74,840 |
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.Asp641=
- Coding
- c.1923C>T
- MANE Select
- NM_020921
- dbSNP
- rs538981711
- Type
- single nucleotide variant
- Location
- chr14:50760333 (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-asp641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown