Variant
IL7R c.538-1G>A
NM_002185.5(IL7R):c.538-1G>A (p.?)
- IVS4, G-A, -1
- p.?
- rs1315265916
- ClinVar classification
- Pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 14 November 2023
- Expert panel
- ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
c.538-1G>A is a splice variant in IL7R: it sits at or near a boundary between an exon and an intron, where it may change how the gene's RNA is put together. ClinVar classifies it as pathogenic for immunodeficiency 104 (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| immunodeficiency 104ClinVar VCV000014841 (opens in a new tab) | Pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 14 November 2023 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in IL7R
c.538-1G>A lies in intron 4, between exons 4 and 5 of the 8 in IL7R's MANE Select transcript, NM_002185.5.
Molecular details
| Gene | IL7R |
|---|---|
| Transcript | NM_002185.5MANE Select |
| Coding DNA change (HGVS c.) | c.538-1G>A |
| Protein change (HGVS p.) | p.? |
| Predicted consequence | Splice site or regionsplice_acceptor_variant (opens in a new tab)coding_transcript_intron_variant |
| Predicted impact | High |
| Position (GRCh38) | chr5:35873479 G>A |
| Position (GRCh37) | chr5:35873581 G>A |
| dbSNP ID | rs1315265916 (opens in a new tab) |
| ClinVar Variation ID | VCV000014841 (opens in a new tab) |
| ClinVar Allele ID | 29880 |
| ClinGen Allele Registry ID | CA359430531 (opens in a new tab) |
| ClinVar name | NM_002185.5(IL7R):c.538-1G>A |
| Other names | IVS4, G-A, -1 |
IL7R c.538-1G>A in other databases
Reports that look at this variant (2)
These Genome Test condition reports include c.538-1G>A among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Other Inborn Errors of Immunity | Immunodeficiency Disease | |
| Severe Combined Immunodeficiency | Severe Combined Immunodeficiency | Autosomal recessive |
Other variants in IL7R
- c.83-2A>TPathogenic3 stars out of 4
- c.221+1G>APathogenic3 stars out of 4
- c.221+2T>GPathogenic3 stars out of 4
- c.537+1G>APathogenic3 stars out of 4
- C118YPathogenic3 stars out of 4
- E79XLikely pathogenic3 stars out of 4
- I121Nfs*8Pathogenic3 stars out of 4
- K119XLikely pathogenic3 stars out of 4
- P132SLikely pathogenic3 stars out of 4
- Q89XLikely pathogenic3 stars out of 4
Limitations
This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant.
Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports.
Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements.
If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor.
Sources & credits
- Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information.
- Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0.
- Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16).
- Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- Difficult regions from the Genome in a Bottle Consortium (release v3.6).
- Transcripts from MANE (release v1.5), NCBI and EMBL-EBI.
- Predicted consequences from mehari (release 0.11.0), with transcript models from cdot.
- Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). IL7R c.538-1G>A (rs1315265916) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/il7r/variants/c-538-1g-a
Dante Labs. IL7R c.538-1G>A (rs1315265916) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/il7r/variants/c-538-1g-a
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