6-52240869-G-T

Position:

• chr6-52240869-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
IL17F	NM_052872.4	c.34-1919C>A		intron_variant		ENST00000336123.5	NP_443104.1
IL17F	XM_011514276.1	c.34-1919C>A		intron_variant			XP_011512578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17F	ENST00000336123.5	c.34-1919C>A		intron_variant		1	NM_052872.4	ENSP00000337432	P1
IL17F	ENST00000699946.1	c.34-1919C>A		intron_variant				ENSP00000514702	P1

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

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.616

Alfa AF: 0.535 Hom.: 2069

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9382084; hg19: chr6-52105667;