2-102100877-C-T

Position:

• chr2-102100877-C-T

Variant summary

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

The NM_001320978.2(IL1R1):​c.-84+30344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,920 control chromosomes in the GnomAD database, including 7,209 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 0.29 (7209 hom., cov: 32)
• Consequence: IL1R1 NM_001320978.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_001320978.2	c.-84+30344C>T		intron_variant			NP_001307907.1
IL1R1	NM_001288706.2	c.-84+30344C>T		intron_variant			NP_001275635.1
IL1R1	XM_011511115.3	c.-181-387C>T		intron_variant			XP_011509417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-84+30344C>T		intron_variant		1		ENSP00000386776.1
IL1R1	ENST00000424272.5	c.-84+30344C>T		intron_variant		5		ENSP00000415366.1
IL1R1	ENST00000452403.5	c.-84+31063C>T		intron_variant		3		ENSP00000401646.1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43474 AN: 151802 Hom.: 7210 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43485 AN: 151920 Hom.: 7209 Cov.: 32 AF XY: 0.286 AC XY: 21262 AN XY: 74230

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.280

Alfa AF: 0.337 Hom.: 18737

Bravo AF: 0.274

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.48
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490571; hg19: chr2-102717337;