NM_002188.3:c.*526A>T

Variant names:

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

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NM_002188.3(IL13):c.*526A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The gene IL13 is a tumor suppressor gene (CancerMine: 1 TSG, 1 driver citations). The gene IL13 is a cancer driver gene (CancerMine: 1 TSG, 1 driver citations). The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: IL13 NM_002188.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 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): ()

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

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

RefSeq Transcripts

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

IL13 NM_002188.3

MANE Select

HGVSc / HGVSpc.*526A>T

Exon rankExon 4 of 4

3_prime_UTR

Prot: NP_002179.2

IL13 NM_001354991.2

HGVSc / HGVSpc.*526A>T

Exon rankExon 5 of 5

3_prime_UTR

Prot: NP_001341920.1UniProt: Q4VB53

IL13 NM_001354992.2

HGVSc / HGVSpc.*526A>T

Exon rankExon 6 of 6

3_prime_UTR

Prot: NP_001341921.1UniProt: Q4VB53

Ensembl Transcripts

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

IL13 ENST00000304506.7

TSL:1MANE Select

HGVSc / HGVSpc.*526A>T

Exon rankExon 4 of 4

3_prime_UTR

Prot: ENSP00000304915.3UniProt: P35225

TH2LCRR ENST00000435042.1

TSL:5

HGVSc / HGVSpn.94+3371T>A

Exon rankIntron 1 of 3

intron

Prot:

IL13 ENST00000459878.5

TSL:3

HGVSc / HGVSpn.*194A>T

Exon rankN/A

downstream_gene

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:0
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:31

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.079
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.96
DANN	Benign	0.79
GPN-Star LLR	N/A	-2.1
GPN-Star score	N/A	2.1
PhyloP100	Benign	-1.2

Showing 7 of 7 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs848;

hg19: chr5-131996500;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar