ENST00000311734.6:c.*389C>T

Variant names:

• chr2-102343821-C-T
• rs3821204
• ENST00000311734.6:c.*389C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000311734.6(IL1RL1):​c.*389C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL1RL1 ENST00000311734.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 29 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000311734.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL1	NM_016232.5	MANE Select	c.970+406C>T		intron	N/A	NP_057316.3
	IL1RL1	NR_104167.2		n.1776C>T		non_coding_transcript_exon	Exon 9 of 9
	IL1RL1	NM_003856.4		c.*389C>T		3_prime_UTR	Exon 8 of 8	NP_003847.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RL1	ENST00000311734.6	TSL:1	c.*389C>T		3_prime_UTR	Exon 8 of 8	ENSP00000310371.2
	IL1RL1	ENST00000233954.6	TSL:1 MANE Select	c.970+406C>T		intron	N/A	ENSP00000233954.1
	IL1RL1	ENST00000409584.5	TSL:5	c.*389C>T		3_prime_UTR	Exon 8 of 8	ENSP00000386618.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 875956 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 406914

African (AFR) AF: 0.00 AC: 0 AN: 18216

American (AMR) AF: 0.00 AC: 0 AN: 4828

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6402

East Asian (EAS) AF: 0.00 AC: 0 AN: 7164

South Asian (SAS) AF: 0.00 AC: 0 AN: 19800

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1476

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1762

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 786830

Other (OTH) AF: 0.00 AC: 0 AN: 29478

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.82
PhyloP100		-2.0

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

Other links and lift over

dbSNP: rs3821204; hg19: chr2-102960281;