chr9-6242950-C-T

Variant names:

• chr9-6242950-C-T
• rs4742170
• NM_033439.4:c.91+1165C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_033439.4(IL33):​c.91+1165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,928 control chromosomes in the GnomAD database, including 28,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.59 (28409 hom., cov: 31)
• Consequence: IL33 NM_033439.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.39
• Publications: 20 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 9-6242950-C-T is Benign according to our data. Variant chr9-6242950-C-T is described in ClinVar as Benign. ClinVar VariationId is 1288261.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

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.91+1165C>T		intron	N/A	NP_254274.1
	IL33	NM_001314044.2		c.91+1165C>T		intron	N/A	NP_001300973.1
	IL33	NM_001314045.2		c.91+1165C>T		intron	N/A	NP_001300974.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL33	ENST00000682010.1	MANE Select	c.91+1165C>T		intron	N/A	ENSP00000507310.1
	IL33	ENST00000381434.7	TSL:1	c.91+1165C>T		intron	N/A	ENSP00000370842.3
	IL33	ENST00000611532.4	TSL:1	c.91+1165C>T		intron	N/A	ENSP00000478858.1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89977 AN: 151810 Hom.: 28399 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.592 AC: 90006 AN: 151928 Hom.: 28409 Cov.: 31 AF XY: 0.600 AC XY: 44521 AN XY: 74254

African (AFR) AF: 0.361 AC: 14947 AN: 41406

American (AMR) AF: 0.716 AC: 10926 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2673 AN: 5160

South Asian (SAS) AF: 0.677 AC: 3254 AN: 4808

European-Finnish (FIN) AF: 0.705 AC: 7439 AN: 10556

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46310 AN: 67952

Other (OTH) AF: 0.636 AC: 1338 AN: 2104

Alfa AF: 0.658 Hom.: 40071

Bravo AF: 0.585

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 18, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 30544846)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.15
PhyloP100		-1.4
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: rs4742170; hg19: chr9-6242950;