chr2-102110201-A-G

Position:

• chr2-102110201-A-G

Variant summary

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

The NM_001320978.2(IL1R1):​c.-84+39668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,872 control chromosomes in the GnomAD database, including 28,943 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 0.61 (28943 hom., cov: 31)
• Consequence: IL1R1 NM_001320978.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

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 = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1R1	NM_001320978.2	c.-84+39668A>G		intron_variant			NP_001307907.1
IL1R1	NM_001320980.2	c.-84+5329A>G		intron_variant			NP_001307909.1
IL1R1	NM_001288706.2	c.-84+39668A>G		intron_variant			NP_001275635.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000409929.5	c.-84+39668A>G		intron_variant		1		ENSP00000386776.1
IL1R1	ENST00000409329.5	c.-84+5329A>G		intron_variant		5		ENSP00000387131.1
IL1R1	ENST00000424272.5	c.-84+39668A>G		intron_variant		5		ENSP00000415366.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92786 AN: 151750 Hom.: 28914 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.612 AC: 92870 AN: 151872 Hom.: 28943 Cov.: 31 AF XY: 0.608 AC XY: 45140 AN XY: 74200

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.586

Alfa AF: 0.581 Hom.: 48526

Bravo AF: 0.620

Asia WGS AF: 0.409 AC: 1425 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	7.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12712127; hg19: chr2-102726661;