rs1157505

Variant names:

• chr9-6216240-C-G
• rs1157505
• NM_033439.4:c.-12+388C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-6216240-C-G
• chr9-6216240-C-T

Variant summary

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

The NM_033439.4(IL33):​c.-12+388C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,132 control chromosomes in the GnomAD database, including 3,045 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 0.17 (3045 hom., cov: 32)
• Consequence: IL33 NM_033439.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 19 publications found

Genes affected

IL33 (HGNC:16028): (interleukin 33) The protein encoded by this gene is a cytokine that binds to the IL1RL1/ST2 receptor. The encoded protein is involved in the maturation of Th2 cells and the activation of mast cells, basophils, eosinophils and natural killer cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL33	NM_033439.4	c.-12+388C>G		intron_variant	Intron 1 of 7	ENST00000682010.1	NP_254274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL33	ENST00000682010.1	c.-12+388C>G		intron_variant	Intron 1 of 7		NM_033439.4	ENSP00000507310.1
IL33	ENST00000417746.6	c.-12+388C>G		intron_variant	Intron 1 of 4	2		ENSP00000394039.2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26485 AN: 152014 Hom.: 3045 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.174 AC: 26480 AN: 152132 Hom.: 3045 Cov.: 32 AF XY: 0.177 AC XY: 13144 AN XY: 74370

African (AFR) AF: 0.0430 AC: 1785 AN: 41522

American (AMR) AF: 0.240 AC: 3676 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5162

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4824

European-Finnish (FIN) AF: 0.174 AC: 1844 AN: 10584

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15379 AN: 67968

Other (OTH) AF: 0.165 AC: 348 AN: 2112

Alfa AF: 0.116 Hom.: 196

Bravo AF: 0.174

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.27
PhyloP100		-1.4
PromoterAI		-0.018	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1157505; hg19: chr9-6216240;