rs439154

chr2-113126824-G-Achr2-113126824-G-Cchr2-113126824-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000259206.9(IL1RN):c.74-865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,974 control chromosomes in the GnomAD database, including 12,887 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12887 hom., cov: 32)
• Consequence: IL1RN ENST00000259206.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

IL1RN (HGNC:6000): (interleukin 1 receptor antagonist) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This protein inhibits the activities of interleukin 1, alpha (IL1A) and interleukin 1, beta (IL1B), and modulates a variety of interleukin 1 related immune and inflammatory responses, particularly in the acute phase of infection and inflammation. This gene and five other closely related cytokine genes form a gene cluster spanning approximately 400 kb on chromosome 2. A polymorphism of this gene is reported to be associated with increased risk of osteoporotic fractures and gastric cancer. Several alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RN	NM_000577.5	c.11-865G>A		intron_variant
IL1RN	NM_001318914.2	c.-38-865G>A		intron_variant
IL1RN	NM_173841.3	c.74-865G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RN	ENST00000259206.9	c.74-865G>A		intron_variant		1
IL1RN	ENST00000354115.6	c.11-865G>A		intron_variant		1		A1
IL1RN	ENST00000361779.7	c.-38-865G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61257 AN: 151856 Hom.: 12874 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.412

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.403 AC: 61310 AN: 151974 Hom.: 12887 Cov.: 32 AF XY: 0.412 AC XY: 30569 AN XY: 74274

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.412

Alfa AF: 0.389 Hom.: 1961

Bravo AF: 0.393

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.3
Dann	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs439154; hg19: chr2-113884401; COSMIC: COSV52080009; COSMIC: COSV52080009;