rs1900287

Variant names:

• chr2-113039988-G-A
• rs1900287
• NM_173178.3:c.-57-8222C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-113039988-G-A
• chr2-113039988-G-C
• chr2-113039988-G-T

Variant summary

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

The NM_173178.3(IL36B):​c.-57-8222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,202 control chromosomes in the GnomAD database, including 48,009 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 0.79 (48009 hom., cov: 33)
• Consequence: IL36B NM_173178.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 5 publications found

Genes affected

IL36B (HGNC:15564): (interleukin 36 beta) The protein encoded by this gene is a member of the interleukin 1 cytokine family. Protein structure modeling indicated that this cytokine may contain a 12-stranded beta-trefoil structure that is conserved between IL1A (IL-A alpha) and IL1B (IL-1 beta). This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. Two alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173178.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL36B	NM_173178.3	MANE Select	c.-57-8222C>T		intron	N/A	NP_775270.1	Q9NZH7-2
	IL36B	NM_014438.5		c.-57-8222C>T		intron	N/A	NP_055253.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL36B	ENST00000327407.2	TSL:1 MANE Select	c.-57-8222C>T		intron	N/A	ENSP00000328420.2	Q9NZH7-2
	IL36B	ENST00000259213.9	TSL:1	c.-57-8222C>T		intron	N/A	ENSP00000259213.4	Q9NZH7-1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119544 AN: 152086 Hom.: 47952 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.786 AC: 119661 AN: 152202 Hom.: 48009 Cov.: 33 AF XY: 0.794 AC XY: 59045 AN XY: 74392

African (AFR) AF: 0.929 AC: 38586 AN: 41548

American (AMR) AF: 0.805 AC: 12315 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2566 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4884 AN: 5188

South Asian (SAS) AF: 0.913 AC: 4412 AN: 4830

European-Finnish (FIN) AF: 0.778 AC: 8229 AN: 10576

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46059 AN: 67978

Other (OTH) AF: 0.790 AC: 1671 AN: 2116

Alfa AF: 0.768 Hom.: 8251

Bravo AF: 0.795

Asia WGS AF: 0.934 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		-0.71
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: rs1900287; hg19: chr2-113797565;