rs3783525

Variant names:

• chr2-112784242-T-A
• rs3783525
• NM_000575.5:c.-9+201A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-112784242-T-A
• chr2-112784242-T-C

Variant summary

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

The NM_000575.5(IL1A):​c.-9+201A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,186 control chromosomes in the GnomAD database, including 37,303 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 0.69 (37303 hom., cov: 33)
• Consequence: IL1A NM_000575.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 19 publications found

Genes affected

IL1A (HGNC:5991): (interleukin 1 alpha) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine is a pleiotropic cytokine involved in various immune responses, inflammatory processes, and hematopoiesis. This cytokine is produced by monocytes and macrophages as a proprotein, which is proteolytically processed and released in response to cell injury, and thus induces apoptosis. This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. It has been suggested that the polymorphism of these genes is associated with rheumatoid arthritis and Alzheimer's disease. [provided by RefSeq, Jul 2008]

ENSG00000299339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1A	NM_000575.5	c.-9+201A>T		intron_variant	Intron 1 of 6	ENST00000263339.4	NP_000566.3
IL1A	NM_001371554.1	c.-9+73A>T		intron_variant	Intron 1 of 6		NP_001358483.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1A	ENST00000263339.4	c.-9+201A>T		intron_variant	Intron 1 of 6	1	NM_000575.5	ENSP00000263339.3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105343 AN: 152068 Hom.: 37264 Cov.: 33

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.693 AC: 105423 AN: 152186 Hom.: 37303 Cov.: 33 AF XY: 0.684 AC XY: 50888 AN XY: 74388

African (AFR) AF: 0.784 AC: 32568 AN: 41530

American (AMR) AF: 0.603 AC: 9222 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5180

South Asian (SAS) AF: 0.696 AC: 3363 AN: 4832

European-Finnish (FIN) AF: 0.598 AC: 6313 AN: 10556

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47511 AN: 68004

Other (OTH) AF: 0.681 AC: 1439 AN: 2114

Alfa AF: 0.695 Hom.: 4352

Bravo AF: 0.691

Asia WGS AF: 0.522 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.24
PhyloP100		-0.55
PromoterAI		0.022	Neutral
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: rs3783525; hg19: chr2-113541819; COSMIC: COSV54518932;