RINT1 p.Thr790=
c.2370T>C · rs36058979 · VCV224935
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 5.44%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.26 | GERP 1.2, phastCons 0.59 |
| Overall | ||
| CADD | 6.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.44%
African / African-American · 4,007/73,710 alleles
Filtering AF
5.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.24%
Overall
0.275%
4,357/1,586,976 alleles · common
exomes 2,093/1,434,632 · genomes 2,264/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.44% | 18 |
| Remaining individualsnot grpmax-eligible | 0.313% | 320 |
| Admixed American | 0.232% | 431 |
| Middle Eastern | 0.0673% | 1,486 |
| South Asian | 0.00462% | 21,654 |
| European (non-Finnish) | 0.00206% | 48,627 |
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
- RINT1
- Protein
- p.Thr790=
- Coding
- c.2370T>C
- MANE Select
- NM_021930
- dbSNP
- rs36058979
- Type
- single nucleotide variant
- Location
- chr7:105567302 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 85.97
- Residue 790
- the rint1/tip20 domain
Similar variants
- RINT1 c.1107+1G>T Likely pathogenic ★★ same type
- RINT1 c.1886+5G>A Uncertain significance ★★ same type
- RINT1 c.516-3C>T Uncertain significance ★★ same type
- RINT1 c.840-12T>A Uncertain significance ★★ same type
- RINT1 c.840-3C>G Uncertain significance ★★ same type
- RINT1 p.Ala138Thr Uncertain significance ★★ ⚠ same type
- RINT1 p.Ala13Val Uncertain significance ★★ ⚠ same type
- RINT1 p.Ala188Ser 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/rint1-p-thr790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown