6-52240869-G-T

Variant names:

• chr6-52240869-G-T
• rs9382084
• NM_052872.4:c.34-1919C>A

Variant summary

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

The NM_052872.4(IL17F):​c.34-1919C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 150,594 control chromosomes in the GnomAD database, including 28,799 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 0.62 (28799 hom., cov: 27)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• 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 (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	NM_052872.4	c.34-1919C>A		intron_variant	Intron 1 of 2	ENST00000336123.5	NP_443104.1
IL17F	XM_011514276.1	c.34-1919C>A		intron_variant	Intron 2 of 3		XP_011512578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17F	ENST00000336123.5	c.34-1919C>A		intron_variant	Intron 1 of 2	1	NM_052872.4	ENSP00000337432.4
IL17F	ENST00000699946.1	c.34-1919C>A		intron_variant	Intron 2 of 3			ENSP00000514702.1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 92864 AN: 150478 Hom.: 28775 Cov.: 27

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.617 AC: 92931 AN: 150594 Hom.: 28799 Cov.: 27 AF XY: 0.618 AC XY: 45413 AN XY: 73436

African (AFR) AF: 0.572 AC: 23305 AN: 40724

American (AMR) AF: 0.512 AC: 7748 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2176 AN: 3464

East Asian (EAS) AF: 0.661 AC: 3392 AN: 5130

South Asian (SAS) AF: 0.650 AC: 3099 AN: 4766

European-Finnish (FIN) AF: 0.670 AC: 6884 AN: 10276

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44200 AN: 67802

Other (OTH) AF: 0.616 AC: 1288 AN: 2092

Alfa AF: 0.600 Hom.: 5875

Bravo AF: 0.601

Asia WGS AF: 0.610 AC: 2123 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	0.79
DANN	Benign	0.38
PhyloP100		-0.19
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: rs9382084; hg19: chr6-52105667;