chr6-52239311-C-A

Position:

• chr6-52239311-C-A

Variant summary

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

The NM_052872.4(IL17F):​c.34-361G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 264,176 control chromosomes in the GnomAD database, including 603 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 0.066 (389 hom., cov: 32)
  • Exomes 𝑓: 0.054 (214 hom.)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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=-0.85).
• 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/exons	MANE	Protein	UniProt
IL17F	NM_052872.4	c.34-361G>T		intron_variant		ENST00000336123.5	NP_443104.1
IL17F	XM_011514276.1	c.34-361G>T		intron_variant			XP_011512578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17F	ENST00000336123.5	c.34-361G>T		intron_variant		1	NM_052872.4	ENSP00000337432.4
IL17F	ENST00000699946.1	c.34-361G>T		intron_variant				ENSP00000514702.1

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10113 AN: 152056 Hom.: 392 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0517

GnomAD4 exome AF: 0.0542 AC: 6068 AN: 112002 Hom.: 214 AF XY: 0.0550 AC XY: 3184 AN XY: 57874

Gnomad4 AFR exome AF: 0.0747

Gnomad4 AMR exome AF: 0.0408

Gnomad4 ASJ exome AF: 0.0398

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.0615

Gnomad4 FIN exome AF: 0.0841

Gnomad4 NFE exome AF: 0.0435

Gnomad4 OTH exome AF: 0.0521

GnomAD4 genome AF: 0.0665 AC: 10118 AN: 152174 Hom.: 389 Cov.: 32 AF XY: 0.0700 AC XY: 5210 AN XY: 74400

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.0484

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0420 Hom.: 62

Bravo AF: 0.0612

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.058
DANN	Benign	0.31

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: rs7771466; hg19: chr6-52104109;