INTS1 p.Ala433=
c.1299G>A · rs143126716 · VCV768126
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.85%, 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 -14 | GERP -2.8 |
| Overall | ||
| CADD | 0.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.85%
African / African-American · 2,888/75,002 alleles
Filtering AF
3.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.69%
Overall
0.21%
3,391/1,613,740 alleles · low-frequency
exomes 1,716/1,461,506 · genomes 1,675/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.85% | 26 |
| Remaining individualsnot grpmax-eligible | 0.275% | 363 |
| Admixed American | 0.257% | 390 |
| Middle Eastern | 0.249% | 402 |
| European (non-Finnish) | 0.0131% | 7,661 |
| South Asian | 0.00878% | 11,385 |
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.Ala433=
- Coding
- c.1299G>A
- MANE Select
- NM_001080453
- dbSNP
- rs143126716
- Type
- single nucleotide variant
- Location
- chr7:1498538 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.49 · 8 PDB
- Residue 433
- an α-helix
Similar variants
- INTS1 p.Ala433Thr Uncertain significance ★ ⚠ same residue
- INTS1 p.Ala433Val 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
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-ala433 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown