6-52245936-C-T

Variant names:

• chr6-52245936-C-T
• rs1889570
• ENST00000699946.1:c.-384G>A

Variant summary

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

The ENST00000699946.1(IL17F):​c.-384G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,770 control chromosomes in the GnomAD database, including 12,741 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 0.40 (12741 hom., cov: 31)
• Consequence: IL17F ENST00000699946.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 16 publications found

Genes affected

IL17F (HGNC:16404): (interleukin 17F) The protein encoded by this gene is a cytokine that shares sequence similarity with IL17. This cytokine is expressed by activated T cells, and has been shown to stimulate the production of several other cytokines, including IL6, IL8, and CSF2/GM_CSF. This cytokine is also found to inhibit the angiogenesis of endothelial cells and induce endothelial cells to produce IL2, TGFB1/TGFB, and monocyte chemoattractant protein-1. [provided by RefSeq, Jul 2008]

IL17F Gene-Disease associations (from GenCC):

• chronic mucocutaneous candidiasis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• candidiasis, familial, 6

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	XM_011514276.1	c.-384G>A		upstream_gene_variant			XP_011512578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17F	ENST00000699946.1	c.-384G>A		upstream_gene_variant				ENSP00000514702.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60830 AN: 151652 Hom.: 12734 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.401 AC: 60865 AN: 151770 Hom.: 12741 Cov.: 31 AF XY: 0.401 AC XY: 29735 AN XY: 74160

African (AFR) AF: 0.280 AC: 11570 AN: 41374

American (AMR) AF: 0.339 AC: 5172 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1950 AN: 5136

South Asian (SAS) AF: 0.496 AC: 2379 AN: 4798

European-Finnish (FIN) AF: 0.448 AC: 4708 AN: 10510

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32267 AN: 67908

Other (OTH) AF: 0.412 AC: 868 AN: 2106

Alfa AF: 0.430 Hom.: 1813

Bravo AF: 0.386

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1889570; hg19: chr6-52110734;