Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 49.7%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.067 | GERP -3.1 |
| Overall | ||
| CADD | 0.567 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
49.7%
East Asian · 22,284/44,862 alleles
Filtering AF
49.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 48.9%
Overall
31.1%
502,618/1,613,906 alleles · common
exomes 458,335/1,461,828 · genomes 44,283/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 49.7% | 2 |
| Admixed American | 46.5% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 35.7% | 3 |
| Remaining individualsnot grpmax-eligible | 31.5% | 3 |
| European (non-Finnish) | 30.9% | 3 |
| Finnishnot grpmax-eligible | 30.4% | 3 |
| Middle Eastern | 27.9% | 4 |
| South Asian | 24.3% | 4 |
| Amishnot grpmax-eligible | 20.6% | 5 |
| African / African-American | 19% | 5 |
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.Ser1030=
- Coding
- c.3090A>T
- MANE Select
- NM_020921
- dbSNP
- rs2073348
- Type
- single nucleotide variant
- Location
- chr14:50757940 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
- Residue 1030
- the 'important for interaction with cep170' region; the 'interacts with dsp' region
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-ser1030 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown