chr2-102100877-C-T

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.857
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL1R1NM_001320978.2 linkuse as main transcriptc.-84+30344C>T intron_variant NP_001307907.1 P14778
IL1R1NM_001288706.2 linkuse as main transcriptc.-84+30344C>T intron_variant NP_001275635.1 P14778B8ZZW4
IL1R1XM_011511115.3 linkuse as main transcriptc.-181-387C>T intron_variant XP_011509417.1 P14778

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL1R1ENST00000409929.5 linkuse as main transcriptc.-84+30344C>T intron_variant 1 ENSP00000386776.1 B8ZZW4
IL1R1ENST00000424272.5 linkuse as main transcriptc.-84+30344C>T intron_variant 5 ENSP00000415366.1 B8ZZ73
IL1R1ENST00000452403.5 linkuse as main transcriptc.-84+31063C>T intron_variant 3 ENSP00000401646.1 C9JW84

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43474
AN:
151802
Hom.:
7210
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.125
Gnomad4 AMR
AF:
0.330
Gnomad4 ASJ
AF:
0.224
Gnomad4 EAS
AF:
0.192
Gnomad4 SAS
AF:
0.256
Gnomad4 FIN
AF:
0.429
Gnomad4 NFE
AF:
0.365
Gnomad4 OTH
AF:
0.280
Alfa
AF:
0.337
Hom.:
18737
Bravo
AF:
0.274
Asia WGS
AF:
0.216
AC:
751
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
0.48
DANN
Benign
0.82

Splicing

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: rs10490571; hg19: chr2-102717337; API