Variant chr2-102351825-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_016232.5(IL1RL1):c.1575T>C(p.Ser525=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,612,504 control chromosomes in the GnomAD database, including 122,739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.45 ( 17710 hom., cov: 30)

Exomes 𝑓: 0.37 ( 105029 hom. )

Consequence

IL1RL1
NM_016232.5 synonymous

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 0.158

Variant links:

Genes affected

IL1RL1 (HGNC:5998): (interleukin 1 receptor like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli, and may be involved in the function of helper T cells. This gene, interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2) and interleukin 1 receptor-like 2 (IL1RL2) form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

IL1RL1 links:

IL18R1 (HGNC:5988): (interleukin 18 receptor 1) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This receptor specifically binds interleukin 18 (IL18), and is essential for IL18 mediated signal transduction. IFN-alpha and IL12 are reported to induce the expression of this receptor in NK and T cells. This gene along with four other members of the interleukin 1 receptor family, including IL1R2, IL1R1, ILRL2 (IL-1Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on chromosome 2q. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

IL18R1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=0.158 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RL1	NM_016232.5 linkuse as main transcript	c.1575T>C	p.Ser525=	synonymous_variant	11/11	ENST00000233954.6	NP_057316.3
IL1RL1	XM_006712839.4 linkuse as main transcript	c.1575T>C	p.Ser525=	synonymous_variant	11/11		XP_006712902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 linkuse as main transcript	c.1575T>C	p.Ser525=	synonymous_variant	11/11	1	NM_016232.5	ENSP00000233954	P1	Q01638-1
IL18R1	ENST00000410040.5 linkuse as main transcript	c.-28-10808T>C		intron_variant		2		ENSP00000386663

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68490

AN:

151754

Hom.:

17681

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.413

GnomAD3 exomes

AF:

0.341

AC:

85650

AN:

251140

Hom.:

17296

AF XY:

0.332

AC XY:

45038

AN XY:

135766

show subpopulations

Gnomad AFR exome

AF:

0.709

Gnomad AMR exome

AF:

0.218

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.115

Gnomad SAS exome

AF:

0.179

Gnomad FIN exome

AF:

0.416

Gnomad NFE exome

AF:

0.379

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.368

AC:

538094

AN:

1460630

Hom.:

105029

Cov.:

AF XY:

0.362

AC XY:

263069

AN XY:

726690

show subpopulations

Gnomad4 AFR exome

AF:

0.714

Gnomad4 AMR exome

AF:

0.230

Gnomad4 ASJ exome

AF:

0.469

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.415

Gnomad4 NFE exome

AF:

0.381

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.451

AC:

68570

AN:

151874

Hom.:

17710

Cov.:

AF XY:

0.444

AC XY:

32981

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.477

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.409

Alfa

AF:

0.395

Hom.:

16054

Bravo

AF:

0.458

Asia WGS

AF:

0.180

AC:

627

AN:

3478

EpiCase

AF:

0.380

EpiControl

AF:

0.383

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Ascending aortic dissection

Other:1

association, no assertion criteria provided

case-control

Beijing Anzhen Hospital, Capital Medical University

Feb 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.1

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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