rs1894399

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000575.5(IL1A):​c.96+116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 727,972 control chromosomes in the GnomAD database, including 32,878 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 0.32 ( 7964 hom., cov: 33)
Exomes 𝑓: 0.29 ( 24914 hom. )

Consequence

IL1A
NM_000575.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL1ANM_000575.5 linkuse as main transcriptc.96+116G>A intron_variant ENST00000263339.4
IL1ANM_001371554.1 linkuse as main transcriptc.96+116G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL1AENST00000263339.4 linkuse as main transcriptc.96+116G>A intron_variant 1 NM_000575.5 P1

Frequencies

GnomAD3 genomes
AF:
0.317
AC:
48232
AN:
151978
Hom.:
7951
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.391
Gnomad AMI
AF:
0.410
Gnomad AMR
AF:
0.292
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.0792
Gnomad SAS
AF:
0.299
Gnomad FIN
AF:
0.316
Gnomad MID
AF:
0.379
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.310
GnomAD4 exome
AF:
0.289
AC:
166467
AN:
575876
Hom.:
24914
AF XY:
0.290
AC XY:
88880
AN XY:
306510
show subpopulations
Gnomad4 AFR exome
AF:
0.384
Gnomad4 AMR exome
AF:
0.244
Gnomad4 ASJ exome
AF:
0.339
Gnomad4 EAS exome
AF:
0.0907
Gnomad4 SAS exome
AF:
0.307
Gnomad4 FIN exome
AF:
0.313
Gnomad4 NFE exome
AF:
0.299
Gnomad4 OTH exome
AF:
0.299
GnomAD4 genome
AF:
0.317
AC:
48287
AN:
152096
Hom.:
7964
Cov.:
33
AF XY:
0.317
AC XY:
23595
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.391
Gnomad4 AMR
AF:
0.292
Gnomad4 ASJ
AF:
0.343
Gnomad4 EAS
AF:
0.0792
Gnomad4 SAS
AF:
0.299
Gnomad4 FIN
AF:
0.316
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.308
Alfa
AF:
0.316
Hom.:
1180
Bravo
AF:
0.316
Asia WGS
AF:
0.214
AC:
747
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
5.2
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1894399; hg19: chr2-113540177; API