chr2-102350446-C-T

Position:

• chr2-102350446-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_016232.5(IL1RL1):​c.1286-1090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.34 (1064 hom., cov: 42)
  • Failed GnomAD Quality Control
• Consequence: IL1RL1 NM_016232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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]

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RL1	NM_016232.5	c.1286-1090C>T		intron_variant		ENST00000233954.6	NP_057316.3
IL1RL1	XM_006712839.4	c.1286-1090C>T		intron_variant			XP_006712902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6	c.1286-1090C>T		intron_variant		1	NM_016232.5	ENSP00000233954	P1
IL18R1	ENST00000410040.5	c.-28-12187C>T		intron_variant		2		ENSP00000386663

Frequencies

GnomAD3 genomes AF: 0.00 AC: 51509 AN: 151184 Hom.: 1063 Cov.: 42 FAILED QC

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.341 AC: 51560 AN: 151304 Hom.: 1064 Cov.: 42 AF XY: 0.336 AC XY: 24835 AN XY: 73964

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.324

Alfa AF: 0.329 Hom.: 138

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs1861245; hg19: chr2-102966906; COSMIC: COSV52120403; COSMIC: COSV52120403;