# NM_001080453.3(INTS1):c.870G>A (p.Thr290=)

https://sugi.bio/variant/ints1-p-thr290

## Summary

**INTS1 p.Thr290= (c.870G>A)** is classified **Benign/Likely benign** in INTS1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-05-24). Rare (popmax 0.599%, afr).

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs201734949 · 4 submitters · rare (popmax 0.599%, afr)

## For patients & families {#patients}

This is a change in the INTS1 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 4 submitters.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [INTS1](https://sugi.bio/atlas/gene/INTS1/) |
| Protein change (HGVS p.) | p.Thr290= |
| Coding change (HGVS c.) | c.870G>A |
| MANE Select transcript | [NM_001080453](https://www.ncbi.nlm.nih.gov/nuccore/NM_001080453) |
| dbSNP | [rs201734949](https://www.ncbi.nlm.nih.gov/snp/rs201734949/) |
| Variant type | single nucleotide variant |
| Location | chr7:1499335-1499335 (GRCh38) |
| ClinVar | [VCV734603](https://www.ncbi.nlm.nih.gov/clinvar/variation/734603/) |

**All HGVS expressions:** `NC_000007.13:g.1538971C>T`, `NC_000007.14:g.1499335C>T`, `NM_001080453.3:c.870G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor gain** (Δ 0.20) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP -20, GERP -2.39 — fast-evolving / accelerated position
- CADD: **PHRED 3.397**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI deltas (raw): acceptor loss **0.06**, donor loss **0.00**, acceptor gain **0.20**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.20**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **0.599%** (afr) · FAF95 0.553% · FAF99 0.535% · 448/74,788 in the highest group · 634/1,598,064 alleles overall — rare (popmax 0.599%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.599% | 167 |
| Remaining individuals (not grpmax-eligible) | 0.0534% | 1,872 |
| Admixed American | 0.051% | 1,962 |
| Middle Eastern | 0.0167% | 5,992 |
| European (non-Finnish) | 0.00981% | 10,192 |
| Finnish (not grpmax-eligible) | 0.00645% | 15,498 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00352% | 28,442 |
| South Asian | 0.00226% | 44,262 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**INTS1** population constraint: LOEUF 0.785, pLI 2.0443e-30, missense-Z -1.9354. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 75.49, 15% of residues very-high.

**8 experimental structure(s)** (PDB): [7CUN](https://www.rcsb.org/structure/7CUN), [7PKS](https://www.rcsb.org/structure/7PKS), [7YCX](https://www.rcsb.org/structure/7YCX), [8RBX](https://www.rcsb.org/structure/8RBX), [8RBZ](https://www.rcsb.org/structure/8RBZ), [8RC4](https://www.rcsb.org/structure/8RC4).

## What this gene does {#gene-function}

*Describes the biological roles of INTS1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*


### Pathways affected {#pathways}

INTS1 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [RNA polymerase II transcribes snRNA genes](https://reactome.org/content/detail/R-HSA-6807505) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** snRNA processing, regulation of transcription elongation by RNA polymerase II, RNA polymerase II transcription initiation surveillance.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-05-24.

**Submitter consensus:** conflicting (2 Likely benign, 1 Benign).

**Submission history:** 10 submissions (2018–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2018-07-19 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-05-24 |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2022-02-11 |
| Dr. Peter K. Rogan Lab, Western University |  | no classification provided | in vitro |  |

**Reported phenotype names (ClinVar):** not provided, INTS1-related disorder, not specified, Colon adenocarcinoma, Uterine corpus endometrial carcinoma, Malignant tumor of urinary bladder, Nonpapillary renal cell carcinoma, Cervical cancer, INTS1-related condition, AllHighlyPenetrant.

## Similar variants {#similar}

Related INTS1 variant pages (same residue, condition, or type): [INTS1 p.Thr290Met](/variant/ints1-p-thr290met), [INTS1 c.3430-2A>C](/variant/ints1-c-3430-minus-2a-c), [INTS1 p.Arg101Ter](/variant/ints1-p-arg101ter), [INTS1 p.Glu182Ter](/variant/ints1-p-glu182ter), [INTS1 c.1283+5G>A](/variant/ints1-c-1283-plus-5g-a), [INTS1 c.2977-5C>T](/variant/ints1-c-2977-minus-5c-t), [INTS1 p.Ala1112Val](/variant/ints1-p-ala1112val), [INTS1 p.Ala1505Val](/variant/ints1-p-ala1505val).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 734603). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*