2-102113847-T-C

Position:

• chr2-102113847-T-C

Variant summary

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

The ENST00000409929.5(IL1R1):​c.-83-40094T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,222 control chromosomes in the GnomAD database, including 54,329 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 0.84 (54329 hom., cov: 32)
• Consequence: IL1R1 ENST00000409929.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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 (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1R1	NM_001288706.2	c.-83-40094T>C		intron_variant
IL1R1	NM_001320978.2	c.-83-40094T>C		intron_variant
IL1R1	NM_001320980.2	c.-84+8975T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1R1	ENST00000409929.5	c.-83-40094T>C		intron_variant		1
IL1R1	ENST00000409329.5	c.-84+8975T>C		intron_variant		5
IL1R1	ENST00000409589.5	c.-84+8975T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128145 AN: 152104 Hom.: 54271 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.843 AC: 128261 AN: 152222 Hom.: 54329 Cov.: 32 AF XY: 0.848 AC XY: 63110 AN XY: 74434

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.813

Alfa AF: 0.794 Hom.: 98315

Bravo AF: 0.842

Asia WGS AF: 0.892 AC: 3102 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	0.67
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887998; hg19: chr2-102730307;