5-132658770-C-T

Variant names:

• chr5-132658770-C-T
• rs1295687
• ENST00000462480.1:n.598C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002188.3(IL13):​c.174+410C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL13 NM_002188.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.26
• Publications: 18 publications found

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]

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13	NM_002188.3	c.174+410C>T		intron_variant	Intron 1 of 3	ENST00000304506.7	NP_002179.2
IL13	NM_001354991.2	c.-22+410C>T		intron_variant	Intron 2 of 4		NP_001341920.1
IL13	NM_001354992.2	c.-22+410C>T		intron_variant	Intron 3 of 5		NP_001341921.1
IL13	NM_001354993.2	c.-21-648C>T		intron_variant	Intron 2 of 4		NP_001341922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13	ENST00000304506.7	c.174+410C>T		intron_variant	Intron 1 of 3	1	NM_002188.3	ENSP00000304915.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 29876 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 15236

African (AFR) AF: 0.00 AC: 0 AN: 1008

American (AMR) AF: 0.00 AC: 0 AN: 2962

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 876

East Asian (EAS) AF: 0.00 AC: 0 AN: 1446

South Asian (SAS) AF: 0.00 AC: 0 AN: 1742

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1208

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 110

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18776

Other (OTH) AF: 0.00 AC: 0 AN: 1748

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0080
DANN	Benign	0.89
PhyloP100		-4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1295687; hg19: chr5-131994462;