Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.4%, afr) — 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. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.4%
African / African-American · 7,764/74,916 alleles
Filtering AF
10.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.1%
Overall
0.54%
8,717/1,613,578 alleles · common
exomes 4,188/1,461,360 · genomes 4,529/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.4% | 10 |
| Remaining individualsnot grpmax-eligible | 0.699% | 143 |
| Admixed American | 0.607% | 165 |
| Middle Eastern | 0.198% | 505 |
| South Asian | 0.0307% | 3,252 |
| European (non-Finnish) | 0.00949% | 10,533 |
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
- SEC62
- Protein
- p.Ala25=
- Coding
- c.75C>G
- MANE Select
- NM_003262
- dbSNP
- rs9290379
- Type
- single nucleotide variant
- Location
- chr3:169975646 (GRCh38)
- Gene constraint
- LOEUF 0.392 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.29 · 1 PDB
Similar variants
- SEC62 p.Ala94= Benign ★★ same type
- SEC62 p.Ala115Asp Uncertain significance ★ ⚠ same type
- SEC62 p.Ala209Val Uncertain significance ★ same type
- SEC62 p.Ala94Val Uncertain significance ★ ⚠ same type
- SEC62 p.Arg339Gln Uncertain significance ★ ⚠ same type
- SEC62 p.Arg347Gly Uncertain significance ★ ⚠ same type
- SEC62 p.Asn129Tyr Uncertain significance ★ ⚠ same type
- SEC62 p.Glu116Gly 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/sec62-p-ala25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown