Variant rs1420101 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016232.5(IL1RL1):c.610+428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,240,744 control chromosomes in the GnomAD database, including 85,591 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 0.35 ( 9542 hom., cov: 29)

Exomes 𝑓: 0.37 ( 76049 hom. )

Consequence

IL1RL1
NM_016232.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.129

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:

IL1RL1 (HGNC:):

IL1RL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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.610+428C>T		intron_variant		ENST00000233954.6	NP_057316.3	Q01638-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 linkuse as main transcript	c.610+428C>T		intron_variant		1	NM_016232.5	ENSP00000233954.1		Q01638-1

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53264

AN:

150574

Hom.:

9536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.367

GnomAD3 exomes

AF:

0.326

AC:

34721

AN:

106446

Hom.:

5834

AF XY:

0.333

AC XY:

19450

AN XY:

58404

show subpopulations

Gnomad AFR exome

AF:

0.296

Gnomad AMR exome

AF:

0.212

Gnomad ASJ exome

AF:

0.298

Gnomad EAS exome

AF:

0.389

Gnomad SAS exome

AF:

0.353

Gnomad FIN exome

AF:

0.309

Gnomad NFE exome

AF:

0.353

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.372

AC:

405350

AN:

1090062

Hom.:

76049

Cov.:

AF XY:

0.372

AC XY:

198512

AN XY:

533282

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.302

Gnomad4 EAS exome

AF:

0.415

Gnomad4 SAS exome

AF:

0.359

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.378

Gnomad4 OTH exome

AF:

0.376

GnomAD4 genome

AF:

0.354

AC:

53305

AN:

150682

Hom.:

9542

Cov.:

AF XY:

0.352

AC XY:

25846

AN XY:

73398

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.292

Gnomad4 ASJ

AF:

0.311

Gnomad4 EAS

AF:

0.437

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.374

Alfa

AF:

0.371

Hom.:

27475

Bravo

AF:

0.347

Asia WGS

AF:

0.416

AC:

1448

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.2

DANN

Benign

0.60

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over