SEC24C p.Ser996=
c.2988C>T · rs145850096 · VCV779116
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.127%, afr)
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 -0.82 | GERP -3.7, phastCons 0.013 |
| Overall | ||
| CADD | 12.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.127%
African / African-American · 95/74,992 alleles
Filtering AF
0.106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0983%
Overall
0.00719%
116/1,613,942 alleles · rare
exomes 60/1,461,846 · genomes 56/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.127% | 789 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Finnishnot grpmax-eligible | 0.00781% | 12,796 |
| Admixed American | 0.00333% | 29,993 |
| South Asian | 0.0011% | 91,062 |
| European (non-Finnish) | 0.000339% | 294,990 |
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.Ser996=
- Coding
- c.2988C>T
- MANE Select
- NM_198597
- dbSNP
- rs145850096
- Type
- single nucleotide variant
- Location
- chr10:73770405 (GRCh38)
- Gene constraint
- LOEUF 0.275 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.29 · 3 PDB
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-ser996 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown