rs848

Variant names:

• chr5-132660808-A-C
• rs848
• NM_002188.3:c.*526A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-132660808-A-C
• chr5-132660808-A-G
• chr5-132660808-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002188.3(IL13):​c.*526A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 158,878 control chromosomes in the GnomAD database, including 38,217 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 0.68 (36320 hom., cov: 31)
  • Exomes 𝑓: 0.72 (1897 hom.)
• Consequence: IL13 NM_002188.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 137 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002188.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13	NM_002188.3	MANE Select	c.*526A>C		3_prime_UTR	Exon 4 of 4	NP_002179.2
	IL13	NM_001354991.2		c.*526A>C		3_prime_UTR	Exon 5 of 5	NP_001341920.1	Q4VB53
	IL13	NM_001354992.2		c.*526A>C		3_prime_UTR	Exon 6 of 6	NP_001341921.1	Q4VB53

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13	ENST00000304506.7	TSL:1 MANE Select	c.*526A>C		3_prime_UTR	Exon 4 of 4	ENSP00000304915.3	P35225
	TH2LCRR	ENST00000435042.1	TSL:5	n.94+3371T>G		intron	N/A
	IL13	ENST00000459878.5	TSL:3	n.*194A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102993 AN: 151830 Hom.: 36321 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.718

GnomAD4 exome AF: 0.721 AC: 4995 AN: 6932 Hom.: 1897 Cov.: 0 AF XY: 0.719 AC XY: 2635 AN XY: 3666

African (AFR) AF: 0.419 AC: 26 AN: 62

American (AMR) AF: 0.534 AC: 884 AN: 1654

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 42 AN: 50

East Asian (EAS) AF: 0.702 AC: 226 AN: 322

South Asian (SAS) AF: 0.735 AC: 478 AN: 650

European-Finnish (FIN) AF: 0.628 AC: 290 AN: 462

Middle Eastern (MID) AF: 0.750 AC: 3 AN: 4

European-Non Finnish (NFE) AF: 0.822 AC: 2868 AN: 3488

Other (OTH) AF: 0.742 AC: 178 AN: 240

GnomAD4 genome AF: 0.678 AC: 103020 AN: 151946 Hom.: 36320 Cov.: 31 AF XY: 0.671 AC XY: 49826 AN XY: 74242

African (AFR) AF: 0.503 AC: 20819 AN: 41378

American (AMR) AF: 0.632 AC: 9655 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3485 AN: 5164

South Asian (SAS) AF: 0.710 AC: 3415 AN: 4812

European-Finnish (FIN) AF: 0.611 AC: 6443 AN: 10552

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54067 AN: 67970

Other (OTH) AF: 0.719 AC: 1521 AN: 2114

Alfa AF: 0.763 Hom.: 56854

Bravo AF: 0.669

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs848; hg19: chr5-131996500;