chr2-102139835-A-G

Position:

• chr2-102139835-A-G

Variant summary

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

The ENST00000409929.5(IL1R1):​c.-83-14106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,252 control chromosomes in the GnomAD database, including 51,606 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 0.82 (51606 hom., cov: 33)
• Consequence: IL1R1 ENST00000409929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_001288706.2	c.-83-14106A>G		intron_variant			NP_001275635.1
IL1R1	NM_001320978.2	c.-83-14106A>G		intron_variant			NP_001307907.1
IL1R1	NM_001320980.2	c.-83-14106A>G		intron_variant			NP_001307909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-83-14106A>G		intron_variant		1		ENSP00000386776
IL1R1	ENST00000409329.5	c.-83-14106A>G		intron_variant		5		ENSP00000387131
IL1R1	ENST00000409589.5	c.-83-14106A>G		intron_variant		5		ENSP00000386555

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124573 AN: 152134 Hom.: 51538 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.819 AC: 124698 AN: 152252 Hom.: 51606 Cov.: 33 AF XY: 0.823 AC XY: 61243 AN XY: 74454

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.781

Alfa AF: 0.802 Hom.: 6125

Bravo AF: 0.819

Asia WGS AF: 0.803 AC: 2796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2041748; hg19: chr2-102756295; COSMIC: COSV68605520; COSMIC: COSV68605520;