Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.94%, afr)
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 -15 | GERP -10 |
| Overall | ||
| CADD | 0.202 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.94%
African / African-American · 2,206/75,024 alleles
Filtering AF
2.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.8%
Overall
0.18%
2,911/1,613,314 alleles · low-frequency
exomes 1,585/1,461,028 · genomes 1,326/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.94% | 34 |
| Remaining individualsnot grpmax-eligible | 0.275% | 363 |
| Admixed American | 0.262% | 382 |
| Middle Eastern | 0.066% | 1,515 |
| European (non-Finnish) | 0.0306% | 3,267 |
| South Asian | 0.00988% | 10,119 |
| East Asian | 0.00446% | 22,436 |
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
- IQCE
- Protein
- p.Ser679=
- Coding
- c.2037C>T
- MANE Select
- NM_152558
- dbSNP
- rs6969432
- Type
- single nucleotide variant
- Location
- chr7:2610111 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
- Residue 679
- the 'disordered' region
Similar variants
- IQCE p.Lys538Arg Uncertain significance ★★ ⚠ same type
- IQCE p.Asp645= Benign/Likely benign ★★ same type
- IQCE p.Leu277= Benign/Likely benign ★★ same type
- IQCE p.Pro586Ser Likely benign ★★ same type
- IQCE p.Met1Ile Likely pathogenic ★ same type
- IQCE p.Trp498Ter Pathogenic ★ same type
- IQCE p.Tyr255Ter Pathogenic ★ same type
- IQCE c.1440+1G>T 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/iqce-p-ser679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown