NIN p.Ala996=
c.2988G>A · rs80291668 · VCV776838
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.09%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.91 | GERP -2.8 |
| Overall | ||
| CADD | 1.384 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.09%
African / African-American · 1,566/75,054 alleles
Filtering AF
2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.97%
Overall
0.111%
1,799/1,614,222 alleles · low-frequency
exomes 906/1,461,880 · genomes 893/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.09% | 48 |
| Admixed American | 0.147% | 682 |
| Remaining individualsnot grpmax-eligible | 0.128% | 781 |
| Middle Eastern | 0.099% | 1,010 |
| European (non-Finnish) | 0.00466% | 21,455 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| East Asian | 0.00223% | 44,880 |
| South Asian | 0.0022% | 45,540 |
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.Ala996=
- Coding
- c.2988G>A
- MANE Select
- NM_020921
- dbSNP
- rs80291668
- Type
- single nucleotide variant
- Location
- chr14:50758042 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
- Residue 996
- the 'important for interaction with cep170' region
Similar variants
- NIN p.Ala996Val Likely benign ★★ same residue
- NIN p.Ala996Gly 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-ala996 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown