rs2069745
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002188.3(IL13):c.175-351G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 299,392 control chromosomes in the GnomAD database, including 127 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 0.021 ( 107 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 20 hom. )
Consequence
IL13
NM_002188.3 intron
NM_002188.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0850
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0693 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13 | NM_002188.3 | c.175-351G>C | intron_variant | ENST00000304506.7 | |||
IL13 | NM_001354991.2 | c.-21-351G>C | intron_variant | ||||
IL13 | NM_001354992.2 | c.-21-351G>C | intron_variant | ||||
IL13 | NM_001354993.2 | c.-21-351G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL13 | ENST00000304506.7 | c.175-351G>C | intron_variant | 1 | NM_002188.3 | P1 | |||
TH2LCRR | ENST00000435042.1 | n.94+5112C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0205 AC: 3112AN: 152132Hom.: 105 Cov.: 32
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GnomAD4 exome AF: 0.00348 AC: 512AN: 147142Hom.: 20 Cov.: 0 AF XY: 0.00288 AC XY: 221AN XY: 76616
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GnomAD4 genome ? AF: 0.0205 AC: 3126AN: 152250Hom.: 107 Cov.: 32 AF XY: 0.0201 AC XY: 1500AN XY: 74454
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at