rs9807989

Variant names:

• chr2-102354740-T-C
• rs9807989
• ENST00000410040.5:c.-28-7893T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-102354740-T-C
• chr2-102354740-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000410040.5(IL18R1):​c.-28-7893T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,952 control chromosomes in the GnomAD database, including 17,707 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 0.45 (17707 hom., cov: 32)
• Consequence: IL18R1 ENST00000410040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822

Genes affected

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL18R1	ENST00000410040.5	c.-28-7893T>C		intron_variant	Intron 1 of 10	2		ENSP00000386663.1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68536 AN: 151834 Hom.: 17678 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.452 AC: 68615 AN: 151952 Hom.: 17707 Cov.: 32 AF XY: 0.444 AC XY: 33008 AN XY: 74270

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.409

Alfa AF: 0.416 Hom.: 1810

Bravo AF: 0.458

Asia WGS AF: 0.181 AC: 630 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9807989; hg19: chr2-102971200; COSMIC: COSV52114115;