rs1317230

Variant names:

• chr9-6251012-C-A
• rs1317230
• NM_033439.4:c.218-128C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-6251012-C-A
• chr9-6251012-C-G
• chr9-6251012-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.218-128C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,206,902 control chromosomes in the GnomAD database, including 53,029 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 0.27 (6425 hom., cov: 31)
  • Exomes 𝑓: 0.29 (46604 hom.)
• Consequence: IL33 NM_033439.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 11 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]

ENSG00000294323 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL33	NM_033439.4	c.218-128C>A		intron_variant	Intron 3 of 7	ENST00000682010.1	NP_254274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL33	ENST00000682010.1	c.218-128C>A		intron_variant	Intron 3 of 7		NM_033439.4	ENSP00000507310.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41560 AN: 151722 Hom.: 6422 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.288 AC: 303679 AN: 1055062 Hom.: 46604 AF XY: 0.291 AC XY: 153016 AN XY: 525884

African (AFR) AF: 0.161 AC: 3946 AN: 24466

American (AMR) AF: 0.514 AC: 13244 AN: 25776

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 4049 AN: 17938

East Asian (EAS) AF: 0.489 AC: 17535 AN: 35854

South Asian (SAS) AF: 0.375 AC: 22453 AN: 59844

European-Finnish (FIN) AF: 0.326 AC: 11458 AN: 35182

Middle Eastern (MID) AF: 0.361 AC: 1126 AN: 3118

European-Non Finnish (NFE) AF: 0.269 AC: 216974 AN: 807364

Other (OTH) AF: 0.283 AC: 12894 AN: 45520

GnomAD4 genome AF: 0.274 AC: 41560 AN: 151840 Hom.: 6425 Cov.: 31 AF XY: 0.283 AC XY: 21008 AN XY: 74192

African (AFR) AF: 0.161 AC: 6648 AN: 41404

American (AMR) AF: 0.423 AC: 6457 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2540 AN: 5140

South Asian (SAS) AF: 0.388 AC: 1866 AN: 4804

European-Finnish (FIN) AF: 0.317 AC: 3340 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19046 AN: 67918

Other (OTH) AF: 0.284 AC: 597 AN: 2102

Alfa AF: 0.266 Hom.: 2710

Bravo AF: 0.278

Asia WGS AF: 0.375 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.29
DANN	Benign	0.28
PhyloP100		-1.7
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: rs1317230; hg19: chr9-6251012; COSMIC: COSV67343560;