Genetic Variant IL1RN:c.11-148G>T (chr2-113119918-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_173841.3(IL1RN):c.11-148G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 713,060 control chromosomes in the GnomAD database, including 243,236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46968 hom., cov: 29)

Exomes 𝑓: 0.83 ( 196268 hom. )

Consequence

IL1RN
NM_173841.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0880

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 2-113119918-G-T is Benign according to our data. Variant chr2-113119918-G-T is described in ClinVar as [Benign]. Clinvar id is 1266807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
IL1RN	NM_173841.3 link	c.11-148G>T	intron_variant	Intron 1 of 5	NP_776213.1	P18510-3
IL1RN	NM_000577.5 link	c.10+1890G>T	intron_variant	Intron 1 of 4	NP_000568.1	P18510-2
IL1RN	NM_001318914.2 link	c.-272-148G>T	intron_variant	Intron 1 of 6	NP_001305843.1	P18510-4A0A024R528

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
IL1RN	ENST00000259206.9 link	c.11-148G>T	intron_variant	Intron 1 of 5	1	ENSP00000259206.5	P18510-3
IL1RN	ENST00000354115.6 link	c.10+1890G>T	intron_variant	Intron 1 of 4	1	ENSP00000329072.3	P18510-2
IL1RN	ENST00000361779.7 link	c.-209-1530G>T	intron_variant	Intron 1 of 5	1	ENSP00000354816.3	P18510-4

Frequencies

GnomAD3 genomes

AF:

0.777

AC:

117834

AN:

151674

Hom.:

46938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.841

Gnomad ASJ

AF:

0.883

Gnomad EAS

AF:

0.457

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.753

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.872

Gnomad OTH

AF:

0.805

GnomAD4 exome

AF:

0.828

AC:

464765

AN:

561268

Hom.:

196268

AF XY:

0.833

AC XY:

248211

AN XY:

297824

show subpopulations

Gnomad4 AFR exome

AF:

0.617

Gnomad4 AMR exome

AF:

0.831

Gnomad4 ASJ exome

AF:

0.883

Gnomad4 EAS exome

AF:

0.418

Gnomad4 SAS exome

AF:

0.884

Gnomad4 FIN exome

AF:

0.762

Gnomad4 NFE exome

AF:

0.874

Gnomad4 OTH exome

AF:

0.827

GnomAD4 genome

AF:

0.777

AC:

117911

AN:

151792

Hom.:

46968

Cov.:

AF XY:

0.773

AC XY:

57327

AN XY:

74176

show subpopulations

Gnomad4 AFR

AF:

0.618

Gnomad4 AMR

AF:

0.841

Gnomad4 ASJ

AF:

0.883

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.878

Gnomad4 FIN

AF:

0.753

Gnomad4 NFE

AF:

0.872

Gnomad4 OTH

AF:

0.807

Alfa

AF:

0.765

Hom.:

6009

Bravo

AF:

0.771

Asia WGS

AF:

0.687

AC:

2389

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

DANN

Benign

0.36

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