rs153109

Variant names:

• chr16-28507775-T-C
• rs153109
• ENST00000568075.1:c.-362-3725A>G

Variant summary

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

The ENST00000568075.1(IL27):​c.-362-3725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,668 control chromosomes in the GnomAD database, including 14,749 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 0.43 (14749 hom., cov: 30)
• Consequence: IL27 ENST00000568075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 126 publications found

Genes affected

IL27 (HGNC:19157): (interleukin 27) The protein encoded by this gene is one of the subunits of a heterodimeric cytokine complex. This protein is related to interleukin 12A (IL12A). It interacts with Epstein-Barr virus induced gene 3 (EBI3), a protein similar to interleukin 12B (IL12B), and forms a complex that has been shown to drive rapid expansion of naive but not memory CD4(+) T cells. The complex is also found to synergize strongly with interleukin 12 to trigger interferon gamma (IFNG) production of naive CD4(+) T cells. The biological effects of this cytokine are mediated by the class I cytokine receptor (WSX1/TCRR). [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL27	ENST00000568075.1	c.-362-3725A>G		intron_variant	Intron 1 of 3	5		ENSP00000455990.1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65479 AN: 151550 Hom.: 14724 Cov.: 30

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.432 AC: 65553 AN: 151668 Hom.: 14749 Cov.: 30 AF XY: 0.433 AC XY: 32053 AN XY: 74100

African (AFR) AF: 0.370 AC: 15312 AN: 41338

American (AMR) AF: 0.479 AC: 7305 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3464

East Asian (EAS) AF: 0.384 AC: 1972 AN: 5132

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4808

European-Finnish (FIN) AF: 0.545 AC: 5724 AN: 10512

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31345 AN: 67868

Other (OTH) AF: 0.397 AC: 832 AN: 2096

Alfa AF: 0.445 Hom.: 19665

Bravo AF: 0.431

Asia WGS AF: 0.404 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs153109; hg19: chr16-28519096;