chr5-132660272-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002188.3(IL13):c.431A>G(p.Gln144Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 1,613,648 control chromosomes in the GnomAD database, including 502,207 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.77 ( 45613 hom., cov: 33)
Exomes 𝑓: 0.79 ( 456594 hom. )
Consequence
IL13
NM_002188.3 missense
NM_002188.3 missense
Scores
13
Clinical Significance
Conservation
PhyloP100: -2.73
Genes affected
IL13 (HGNC:5973): (interleukin 13) This gene encodes an immunoregulatory cytokine produced primarily by activated Th2 cells. This cytokine is involved in several stages of B-cell maturation and differentiation. It up-regulates CD23 and MHC class II expression, and promotes IgE isotype switching of B cells. This cytokine down-regulates macrophage activity, thereby inhibits the production of pro-inflammatory cytokines and chemokines. This cytokine is found to be critical to the pathogenesis of allergen-induced asthma but operates through mechanisms independent of IgE and eosinophils. This gene, IL3, IL5, IL4, and CSF2 form a cytokine gene cluster on chromosome 5q, with this gene particularly close to IL4. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=8.8788516E-7).
BP6
?
Variant 5-132660272-A-G is Benign according to our data. Variant chr5-132660272-A-G is described in ClinVar as [Benign]. Clinvar id is 14673.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13 | NM_002188.3 | c.431A>G | p.Gln144Arg | missense_variant | 4/4 | ENST00000304506.7 | |
IL13 | NM_001354991.2 | c.236A>G | p.Gln79Arg | missense_variant | 5/5 | ||
IL13 | NM_001354992.2 | c.236A>G | p.Gln79Arg | missense_variant | 6/6 | ||
IL13 | NM_001354993.2 | c.236A>G | p.Gln79Arg | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13 | ENST00000304506.7 | c.431A>G | p.Gln144Arg | missense_variant | 4/4 | 1 | NM_002188.3 | P1 | |
TH2LCRR | ENST00000435042.1 | n.94+3907T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.770 AC: 117104AN: 152080Hom.: 45591 Cov.: 33
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GnomAD3 exomes AF: 0.721 AC: 180758AN: 250830Hom.: 67299 AF XY: 0.730 AC XY: 99024AN XY: 135632
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GnomAD4 exome AF: 0.786 AC: 1149254AN: 1461450Hom.: 456594 Cov.: 62 AF XY: 0.785 AC XY: 570680AN XY: 727054
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GnomAD4 genome ? AF: 0.770 AC: 117176AN: 152198Hom.: 45613 Cov.: 33 AF XY: 0.759 AC XY: 56459AN XY: 74410
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3021
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3159
ESP6500AA
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3647
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6923
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88995
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
IL13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inherited susceptibility to asthma Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Allergic rhinitis, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Mar 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P
PrimateAI
Benign
T
Sift4G
Benign
T;T
Vest4
MPC
0.15
ClinPred
T
GERP RS
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