rs3806798

Variant names:

• chr4-141636126-T-A
• rs3806798
• ENST00000887022.1:c.-477T>A

Variant summary

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

The ENST00000887022.1(IL15):​c.-477T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,210 control chromosomes in the GnomAD database, including 781 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 0.089 (781 hom., cov: 32)
• Consequence: IL15 ENST00000887022.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 13 publications found

Genes affected

IL15 (HGNC:5977): (interleukin 15) The protein encoded by this gene is a cytokine that regulates T and natural killer cell activation and proliferation. This cytokine and interleukine 2 share many biological activities. They are found to bind common hematopoietin receptor subunits, and may compete for the same receptor, and thus negatively regulate each other's activity. The number of CD8+ memory cells is shown to be controlled by a balance between this cytokine and IL2. This cytokine induces the activation of JAK kinases, as well as the phosphorylation and activation of transcription activators STAT3, STAT5, and STAT6. Studies of the mouse counterpart suggested that this cytokine may increase the expression of apoptosis inhibitor BCL2L1/BCL-x(L), possibly through the transcription activation activity of STAT6, and thus prevent apoptosis. Alternatively spliced transcript variants of this gene have been reported. [provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000887022.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL15	ENST00000887022.1		c.-477T>A		upstream_gene	N/A	ENSP00000557081.1
	IL15	ENST00000887023.1		c.-532T>A		upstream_gene	N/A	ENSP00000557082.1
	IL15	ENST00000887024.1		c.-511T>A		upstream_gene	N/A	ENSP00000557083.1

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13558 AN: 152092 Hom.: 779 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0891 AC: 13564 AN: 152210 Hom.: 781 Cov.: 32 AF XY: 0.0907 AC XY: 6752 AN XY: 74416

African (AFR) AF: 0.0220 AC: 916 AN: 41556

American (AMR) AF: 0.0688 AC: 1053 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3468

East Asian (EAS) AF: 0.123 AC: 637 AN: 5164

South Asian (SAS) AF: 0.191 AC: 917 AN: 4810

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10606

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7868 AN: 67992

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.104 Hom.: 139

Bravo AF: 0.0825

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.43
PhyloP100		-1.0
PromoterAI		-0.034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3806798; hg19: chr4-142557279;