2-102100877-C-T

Variant names:

• chr2-102100877-C-T
• rs10490571
• ENST00000409929.5:c.-84+30344C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320978.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	NM_001320978.2		c.-84+30344C>T		intron	N/A	NP_001307907.1	P14778
	IL1R1	NM_001288706.2		c.-84+30344C>T		intron	N/A	NP_001275635.1	B8ZZW4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	ENST00000409929.5	TSL:1	c.-84+30344C>T		intron	N/A	ENSP00000386776.1	B8ZZW4
	IL1R1	ENST00000853658.1		c.-84+36739C>T		intron	N/A	ENSP00000523717.1
	IL1R1	ENST00000853659.1		c.-84+30344C>T		intron	N/A	ENSP00000523718.1

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

African (AFR) AF: 0.125 AC: 5168 AN: 41436

American (AMR) AF: 0.330 AC: 5035 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 777 AN: 3464

East Asian (EAS) AF: 0.192 AC: 989 AN: 5162

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4820

European-Finnish (FIN) AF: 0.429 AC: 4511 AN: 10520

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24774 AN: 67934

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.328 Hom.: 27723

Bravo AF: 0.274

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.48
DANN	Benign	0.82
PhyloP100		-0.86
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10490571; hg19: chr2-102717337;