2-102189103-A-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001351449.2(IL1RL2):c.-172A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
IL1RL2
NM_001351449.2 5_prime_UTR_premature_start_codon_gain
NM_001351449.2 5_prime_UTR_premature_start_codon_gain
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 1.81
Genes affected
IL1RL2 (HGNC:5999): (interleukin 1 receptor like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. An experiment with transient gene expression demonstrated that this receptor was incapable of binding to interleukin 1 alpha and interleukin 1 beta with high affinity. This gene and four other interleukin 1 receptor family genes, including interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2), interleukin 1 receptor-like 1 (IL1RL1), and interleukin 18 receptor 1 (IL18R1), form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09991172).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RL2 | ENST00000264257.7 | c.86A>T | p.Asn29Ile | missense_variant | 3/12 | 1 | NM_003854.4 | ENSP00000264257.2 | ||
IL1RL2 | ENST00000441515.3 | c.138+1178A>T | intron_variant | 1 | ENSP00000413348.2 | |||||
IL1RL2 | ENST00000421464.1 | c.86A>T | p.Asn29Ile | missense_variant | 3/5 | 5 | ENSP00000387611.1 | |||
IL1RL2 | ENST00000481806.1 | n.151+1178A>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251234Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135812
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461622Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727128
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.86A>T (p.N29I) alteration is located in exon 3 (coding exon 2) of the IL1RL2 gene. This alteration results from a A to T substitution at nucleotide position 86, causing the asparagine (N) at amino acid position 29 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;D
Polyphen
B;.
Vest4
MutPred
Gain of ubiquitination at K28 (P = 0.0619);Gain of ubiquitination at K28 (P = 0.0619);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at