9-6256292-G-C

Variant names:

• chr9-6256292-G-C
• rs1048274
• NM_033439.4:c.*124G>C

Variant summary

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

The NM_033439.4(IL33):​c.*124G>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 0.00000198 in 505,882 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000020 (0 hom.)
• Consequence: IL33 NM_033439.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 0 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: 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=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033439.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL33	NM_033439.4	MANE Select	c.*124G>C		3_prime_UTR	Exon 8 of 8	NP_254274.1
	IL33	NM_001314044.2		c.*124G>C		3_prime_UTR	Exon 8 of 8	NP_001300973.1
	IL33	NM_001314045.2		c.*124G>C		3_prime_UTR	Exon 8 of 8	NP_001300974.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL33	ENST00000682010.1	MANE Select	c.*124G>C		3_prime_UTR	Exon 8 of 8	ENSP00000507310.1
	IL33	ENST00000381434.7	TSL:1	c.*124G>C		3_prime_UTR	Exon 7 of 7	ENSP00000370842.3
	IL33	ENST00000456383.3	TSL:5	c.*124G>C		3_prime_UTR	Exon 6 of 6	ENSP00000414238.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000198 AC: 1 AN: 505882 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 266012

African (AFR) AF: 0.0000748 AC: 1 AN: 13376

American (AMR) AF: 0.00 AC: 0 AN: 19198

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14364

East Asian (EAS) AF: 0.00 AC: 0 AN: 31802

South Asian (SAS) AF: 0.00 AC: 0 AN: 43694

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36282

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2074

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 317388

Other (OTH) AF: 0.00 AC: 0 AN: 27704

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.82
PhyloP100		0.18

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: rs1048274; hg19: chr9-6256292;