rs153109

Positions:

• chr16-28507775-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL27	ENST00000568075.1	c.-362-3725A>G		intron_variant		5

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

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.397

Alfa AF: 0.447 Hom.: 15273

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs153109; hg19: chr16-28519096;