# NM_001080453.3(INTS1):c.4207G>A (p.Val1403Met)

https://sugi.bio/variant/ints1-p-val1403met

## Summary

**INTS1 p.Val1403Met (c.4207G>A)** is classified **Benign/Likely benign** in INTS1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-01). AlphaMissense: likely benign (0.1136); Rare (popmax 0.868%, mid).

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs191952781 · 2 submitters · AlphaMissense likely benign · rare (popmax 0.868%, mid)

## 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 2 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.Val1403Met |
| Coding change (HGVS c.) | c.4207G>A |
| MANE Select transcript | [NM_001080453](https://www.ncbi.nlm.nih.gov/nuccore/NM_001080453) |
| dbSNP | [rs191952781](https://www.ncbi.nlm.nih.gov/snp/rs191952781/) |
| Variant type | single nucleotide variant |
| Location | chr7:1479552-1479552 (GRCh38) |
| ClinVar | [VCV2657192](https://www.ncbi.nlm.nih.gov/clinvar/variation/2657192/) |

**All HGVS expressions:** `NC_000007.13:g.1519188C>T`, `NC_000007.14:g.1479552C>T`, `NM_001080453.3:c.4207G>A`, `NM_015674.1:c.724G>A`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.1136)
- REVEL 0.106 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.372 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- SpliceAI predicts **donor loss** (Δ 0.24) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 1.028, GERP 1.38, phastCons 0.471 — weakly conserved position
- CADD: **PHRED 16.11**. 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.*
- Regional missense constraint: **o/e 1.09** across the covering region of the MANE Select transcript (1,470,580–1,482,592), spanning 12,012 bp. Chi-square p 0.001. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.00**, donor loss **0.24**, acceptor gain **0.02**, donor gain **0.00**. Largest is donor loss, 1 bp away.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.02**, donor gain **0.00**.
  Masked SpliceAI — what Ensembl VEP and the Broad lookup serve by default — is below the reporting threshold here, so those tools show **no splice signal** for this allele. Masking zeroes a loss scored against a position that is not an annotated splice site, and a gain that merely strengthens an existing one, so the raw score above is describing a cryptic site rather than the site the variant sits on. *No ACMG code is assigned either way.*
- Population frequency (gnomAD v4.1): grpmax **0.868%** (mid) · FAF95 0.678% · FAF99 0.61% · 51/5,878 in the highest group · 1,399/1,554,284 alleles overall — rare (popmax 0.868%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Amish (not grpmax-eligible) | 16.6% | 6 |
| Ashkenazi Jewish (not grpmax-eligible) | 1.04% | 96 |
| Middle Eastern (grpmax) | 0.868% | 115 |
| Remaining individuals (not grpmax-eligible) | 0.205% | 487 |
| Admixed American | 0.137% | 732 |
| South Asian | 0.122% | 819 |
| European (non-Finnish) | 0.0504% | 1,984 |
| African / African-American | 0.0259% | 3,865 |
| Finnish (not grpmax-eligible) | 0.00177% | 56,450 |

Amish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

Residue **1403** lies in an α-helix.

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 2026-01-01.

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

**Submission history:** 2 submissions (2024–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| CeGaT Center for Human Genetics Tuebingen | Benign | criteria provided, single submitter | clinical testing | 2026-01-01 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-10-09 |

**Reported phenotype names (ClinVar):** not provided, not specified, none provided, AllHighlyPenetrant.

## Similar variants {#similar}

Related INTS1 variant pages (same residue, condition, or type): [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), [INTS1 p.Ala1854Val](/variant/ints1-p-ala1854val).

### 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 2657192). 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.*