rs16347

chr2-112774138-T-TTGAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000575.5(IL1A):c.*928_*929insTTCA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,582 control chromosomes in the GnomAD database, including 36,882 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.69 (36882 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: IL1A NM_000575.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.453

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-112774138-T-TTGAA is Benign according to our data. Variant chr2-112774138-T-TTGAA is described in ClinVar as [Benign]. Clinvar id is 1245422.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1A	NM_000575.5	c.*928_*929insTTCA		3_prime_UTR_variant	7/7	ENST00000263339.4
IL1A	NM_001371554.1	c.*928_*929insTTCA		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1A	ENST00000263339.4	c.*928_*929insTTCA		3_prime_UTR_variant	7/7	1	NM_000575.5	P1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104575 AN: 151464 Hom.: 36843 Cov.: 0

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.682

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.690 AC: 104655 AN: 151582 Hom.: 36882 Cov.: 0 AF XY: 0.682 AC XY: 50488 AN XY: 74060

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.677

Alfa AF: 0.695 Hom.: 3978

Bravo AF: 0.687

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 19, 2019

This variant is associated with the following publications: (PMID: 24839866, 26239639, 2571723, 24748463, 28627263, 19917630, 25966251, 25195148, 25981582, 23900673, 21154765, 29145255, 23542780, 25955681, 29023981, 24453029) -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16347; hg19: chr2-113531715;