INTS1 p.Ser2094=
c.6282G>A · rs149670463 · VCV789292
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.32%, mid)
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 -16 | GERP -3.4 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.32%
Middle Eastern · 79/5,994 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.998%
Overall
0.155%
2,448/1,581,728 alleles · low-frequency
exomes 2,209/1,429,368 · genomes 239/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.32% | 76 |
| Ashkenazi Jewishnot grpmax-eligible | 1.25% | 80 |
| South Asian | 0.968% | 103 |
| Remaining individualsnot grpmax-eligible | 0.253% | 396 |
| Admixed American | 0.169% | 591 |
| European (non-Finnish) | 0.0778% | 1,285 |
| African / African-American | 0.0175% | 5,720 |
| Finnishnot grpmax-eligible | 0.00667% | 14,995 |
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.Ser2094=
- Coding
- c.6282G>A
- MANE Select
- NM_001080453
- dbSNP
- rs149670463
- Type
- single nucleotide variant
- Location
- chr7:1471198 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.49 · 8 PDB
- Residue 2094
- a UniProt-annotated variant site (in ndcagf; decreased protein abundance); a UniProt-annotated variant site (in ndcagf)
Similar variants
- INTS1 p.Ser2094Leu Uncertain significance ★ ⚠ same residue
- INTS1 c.3430-2A>C Likely pathogenic ★★ same type
- INTS1 p.Arg101Ter Likely pathogenic ★★ same type
- INTS1 p.Glu182Ter Likely pathogenic ★★ same type
- INTS1 c.1283+5G>A Uncertain significance ★★ same type
- INTS1 c.2977-5C>T Uncertain significance ★★ same type
- INTS1 p.Ala1112Val Uncertain significance ★★ ⚠ same type
- INTS1 p.Ala1505Val 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/ints1-p-ser2094 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown