chr6-52239384-C-T

Variant names:

• chr6-52239384-C-T
• rs7771511
• NM_052872.4:c.34-434G>A

Variant summary

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

The NM_052872.4(IL17F):​c.34-434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,156 control chromosomes in the GnomAD database, including 398 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 0.068 (398 hom., cov: 32)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	NM_052872.4	c.34-434G>A		intron_variant	Intron 1 of 2	ENST00000336123.5	NP_443104.1
IL17F	XM_011514276.1	c.34-434G>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.34-434G>A		intron_variant	Intron 1 of 2	1	NM_052872.4	ENSP00000337432.4
IL17F	ENST00000699946.1	c.34-434G>A		intron_variant	Intron 2 of 3			ENSP00000514702.1
IL17F	ENST00000478427.1	n.-217G>A		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10296 AN: 152038 Hom.: 401 Cov.: 32

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0677 AC: 10301 AN: 152156 Hom.: 398 Cov.: 32 AF XY: 0.0713 AC XY: 5307 AN XY: 74394

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0575 Hom.: 45

Bravo AF: 0.0624

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.79

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: rs7771511; hg19: chr6-52104182;