6-52243264-G-A

Position:

• chr6-52243264-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052872.4(IL17F):​c.33+1133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,150 control chromosomes in the GnomAD database, including 42,882 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 0.75 (42882 hom., cov: 32)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17F	NM_052872.4	c.33+1133C>T		intron_variant		ENST00000336123.5
IL17F	XM_011514276.1	c.33+1133C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17F	ENST00000336123.5	c.33+1133C>T		intron_variant		1	NM_052872.4	P1
IL17F	ENST00000699946.1	c.33+1133C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113848 AN: 152032 Hom.: 42845 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.749 AC: 113936 AN: 152150 Hom.: 42882 Cov.: 32 AF XY: 0.749 AC XY: 55682 AN XY: 74384

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.741

Alfa AF: 0.720 Hom.: 6687

Bravo AF: 0.739

Asia WGS AF: 0.772 AC: 2686 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	1.9
DANN	Benign	0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1266828; hg19: chr6-52108062;