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NM_173842.3(IL1RN):c.68C>T (p.Thr23Met) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 30, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003224503.2

Allele description [Variation Report for NM_173842.3(IL1RN):c.68C>T (p.Thr23Met)]

NM_173842.3(IL1RN):c.68C>T (p.Thr23Met)

Gene:
IL1RN:interleukin 1 receptor antagonist [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q14.1
Genomic location:
Preferred name:
NM_173842.3(IL1RN):c.68C>T (p.Thr23Met)
HGVS:
  • NC_000002.12:g.113127692C>T
  • NG_021240.1:g.14800C>T
  • NM_000577.5:c.14C>T
  • NM_001318914.2:c.-35C>T
  • NM_001379360.1:c.-35C>T
  • NM_173841.3:c.77C>T
  • NM_173842.3:c.68C>TMANE SELECT
  • NM_173843.3:c.-35C>T
  • NP_000568.1:p.Thr5Met
  • NP_776213.1:p.Thr26Met
  • NP_776213.1:p.Thr26Met
  • NP_776214.1:p.Thr23Met
  • LRG_188t1:c.77C>T
  • LRG_188:g.14800C>T
  • LRG_188p1:p.Thr26Met
  • NC_000002.11:g.113885269C>T
  • NM_173841.2:c.77C>T
Protein change:
T23M
Links:
dbSNP: rs55860727
NCBI 1000 Genomes Browser:
rs55860727
Molecular consequence:
  • NM_001318914.2:c.-35C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001379360.1:c.-35C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_173843.3:c.-35C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000577.5:c.14C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173841.3:c.77C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173842.3:c.68C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Microvascular complications of diabetes, susceptibility to, 4
Synonyms:
Microvascular complications of diabetes 4
Identifiers:
MONDO: MONDO:0012966; MedGen: C2675112; OMIM: 612628
Name:
Sterile multifocal osteomyelitis with periostitis and pustulosis
Synonyms:
CHRONIC RECURRENT MULTIFOCAL OSTEOMYELITIS 2, WITH PERIOSTITIS AND PUSTULOSIS
Identifiers:
MONDO: MONDO:0013021; MedGen: C2748507; Orphanet: 210115; OMIM: 612852
Name:
Gastric cancer
Synonyms:
Stomach cancer; Malignant tumor of stomach
Identifiers:
MONDO: MONDO:0001056; MeSH: D013274; MedGen: C0024623; OMIM: 613659; Human Phenotype Ontology: HP:0012126

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003920062Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 30, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920062.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

IL1RN NM_173841.2 exon 3 p.Thr26Met (c.77C>T): This variant has not been reported in the literature, but is present in 0.04% (13/30616) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/2-113885269-C-T). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024