NCSTN p.Ser67=
c.201T>C · rs34676243 · VCV788844
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.94%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.47 | GERP -4.7, phastCons 0.14 |
| Overall | ||
| CADD | 7.227 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.94%
African / African-American · 3,706/75,034 alleles
Filtering AF
4.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.75%
Overall
0.263%
4,244/1,614,178 alleles · low-frequency
exomes 2,147/1,461,878 · genomes 2,097/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.94% | 20 |
| Middle Eastern | 0.611% | 164 |
| Admixed American | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.354% | 283 |
| South Asian | 0.00659% | 15,180 |
| European (non-Finnish) | 0.00373% | 26,819 |
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
- NCSTN
- Protein
- p.Ser67=
- Coding
- c.201T>C
- MANE Select
- NM_015331
- dbSNP
- rs34676243
- Type
- single nucleotide variant
- Location
- chr1:160349009 (GRCh38)
- Gene constraint
- LOEUF 0.343 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.73 · 30 PDB
Similar variants
- NCSTN p.Ser67Thr Uncertain significance ★★ ⚠ same residue
- NCSTN p.Ser67Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- NCSTN p.Ala207Pro Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala298Thr Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala484Thr Uncertain significance ★★ same type
- NCSTN p.Ala48Ser Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala497Val Uncertain significance ★★ ⚠ same type
- NCSTN p.Ala664Gly 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/ncstn-p-ser67 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown