Variant chr2-113133835-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173842.3(IL1RN):c.*964G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,686 control chromosomes in the GnomAD database, including 6,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6831 hom., cov: 32)

Exomes 𝑓: 0.29 ( 23 hom. )

Consequence

IL1RN
NM_173842.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.282

Variant links:

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]

IL1RN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 2-113133835-G-A is Benign according to our data. Variant chr2-113133835-G-A is described in ClinVar as [Benign]. Clinvar id is 330845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RN	NM_173842.3 linkuse as main transcript	c.*964G>A		3_prime_UTR_variant	4/4	ENST00000409930.4	NP_776214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RN	ENST00000409930.4 linkuse as main transcript	c.*964G>A		3_prime_UTR_variant	4/4	1	NM_173842.3	ENSP00000387173	P4	P18510-1

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43948

AN:

151910

Hom.:

6818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.312

GnomAD4 exome

AF:

0.292

AC:

192

AN:

658

Hom.:

Cov.:

AF XY:

0.290

AC XY:

116

AN XY:

400

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.302

Gnomad4 NFE exome

AF:

0.269

Gnomad4 OTH exome

AF:

0.313

GnomAD4 genome

AF:

0.289

AC:

43987

AN:

152028

Hom.:

6831

Cov.:

AF XY:

0.293

AC XY:

21792

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.199

Gnomad4 AMR

AF:

0.442

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.284

Gnomad4 NFE

AF:

0.301

Gnomad4 OTH

AF:

0.311

Alfa

AF:

0.304

Hom.:

11904

Bravo

AF:

0.296

Asia WGS

AF:

0.348

AC:

1210

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Sterile multifocal osteomyelitis with periostitis and pustulosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.7

DANN

Benign

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over