rs13019803

Variant names:

• chr2-102159742-C-T
• rs13019803
• NM_000877.4:c.61+1957C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000877.4(IL1R1):​c.61+1957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,138 control chromosomes in the GnomAD database, including 2,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.14 (2116 hom., cov: 32)
• Consequence: IL1R1 NM_000877.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 0.305
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000877.4. 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_000877.4	MANE Select	c.61+1957C>T		intron	N/A	NP_000868.1	P14778
	IL1R1	NM_001320978.2		c.61+1957C>T		intron	N/A	NP_001307907.1	P14778
	IL1R1	NM_001320980.2		c.61+1957C>T		intron	N/A	NP_001307909.1	P14778

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1R1	ENST00000410023.6	TSL:1 MANE Select	c.61+1957C>T		intron	N/A	ENSP00000386380.1	P14778
	IL1R1	ENST00000409929.5	TSL:1	c.61+1957C>T		intron	N/A	ENSP00000386776.1	B8ZZW4
	IL1R1	ENST00000853658.1		c.61+1957C>T		intron	N/A	ENSP00000523717.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21349 AN: 152020 Hom.: 2111 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.141 AC: 21386 AN: 152138 Hom.: 2116 Cov.: 32 AF XY: 0.141 AC XY: 10463 AN XY: 74386

African (AFR) AF: 0.273 AC: 11330 AN: 41440

American (AMR) AF: 0.144 AC: 2207 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3472

East Asian (EAS) AF: 0.164 AC: 848 AN: 5166

South Asian (SAS) AF: 0.0683 AC: 329 AN: 4820

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10612

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5381 AN: 68020

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.106 Hom.: 2957

Bravo AF: 0.155

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Ascending aortic dissection (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.37
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13019803; hg19: chr2-102776202;