SEC24C p.Asn2=
c.6C>T · VCV4161771
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00383%, nfe)
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 -1.1 | GERP -2.6, phastCons 0.002 |
| Overall | ||
| CADD | 6.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00383%
European (non-Finnish) · 45/1,175,002 alleles
Filtering AF
0.00292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00261%
Overall
0.00293%
47/1,604,788 alleles · very rare
exomes 42/1,452,534 · genomes 5/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00383% | 26,111 |
| African / African-American | 0.00268% | 37,326 |
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
- SEC24C
- Protein
- p.Asn2=
- Coding
- c.6C>T
- MANE Select
- NM_198597
- Type
- single nucleotide variant
- Location
- chr10:73746838 (GRCh38)
- Gene constraint
- LOEUF 0.275 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.29 · 3 PDB
- Residue 2
- the 'disordered' region
Similar variants
- SEC24C c.1800-7T>C Benign ★★ same type
- SEC24C c.3145-4G>A Benign ★★ same type
- SEC24C c.850+10T>G Benign ★★ same type
- SEC24C p.Ala566= Benign ★★ same type
- SEC24C p.Gly257= Benign/Likely benign ★★ same type
- SEC24C p.Pro255Ala Benign ★★ same type
- SEC24C p.Pro958= Likely benign ★★ same type
- SEC24C p.Thr870= Likely benign ★★ 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/sec24c-p-asn2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown