INTS1 p.Glu1008del
c.3019GAG[1] · rs552723932 · VCV810053
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.8%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 18.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.8%
Middle Eastern · 109/6,062 alleles
Filtering AF
1.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.42%
Overall
0.0499%
804/1,612,674 alleles · low-frequency
exomes 731/1,460,516 · genomes 73/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.8% | 56 |
| Remaining individualsnot grpmax-eligible | 0.118% | 844 |
| South Asian | 0.0878% | 1,138 |
| Admixed American | 0.0633% | 1,579 |
| European (non-Finnish) | 0.0404% | 2,473 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,700 |
| African / African-American | 0.024% | 4,166 |
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
- INTS1
- Protein
- p.Glu1008del
- Coding
- c.3019GAG[1]
- MANE Select
- NM_001080453
- dbSNP
- rs552723932
- Type
- Microsatellite
- Location
- chr7:1485422 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.49 · 8 PDB
Similar variants
- INTS1 p.Cys643fs Pathogenic ★ same type
- INTS1 p.Ser2026fs Uncertain significance ★ same type
- INTS1 p.Tyr625del Uncertain significance ★ same type
- INTS1 c.6185-15CT[2] 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/ints1-p-glu1008del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown