Variant rs10173081 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+60C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,354,726 control chromosomes in the GnomAD database, including 15,464 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 0.17 ( 2647 hom., cov: 32)

Exomes 𝑓: 0.14 ( 12817 hom. )

Consequence

IL1RL1
NM_016232.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.43

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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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+60C>T		intron_variant		ENST00000233954.6	NP_057316.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 linkuse as main transcript	c.610+60C>T		intron_variant		1	NM_016232.5	ENSP00000233954	P1	Q01638-1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26509

AN:

151924

Hom.:

2644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.0949

Gnomad SAS

AF:

0.0724

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.141

AC:

170057

AN:

1202684

Hom.:

12817

AF XY:

0.140

AC XY:

83491

AN XY:

596870

show subpopulations

Gnomad4 AFR exome

AF:

0.276

Gnomad4 AMR exome

AF:

0.0915

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.0661

Gnomad4 FIN exome

AF:

0.166

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.144

GnomAD4 genome

AF:

0.175

AC:

26533

AN:

152042

Hom.:

2647

Cov.:

AF XY:

0.172

AC XY:

12816

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.0951

Gnomad4 SAS

AF:

0.0723

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.144

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.147

Hom.:

330

Bravo

AF:

0.174

Asia WGS

AF:

0.0890

AC:

311

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.10

DANN

Benign

0.62

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