rs12203582

Variant names:

• chr6-52240759-G-A
• rs12203582
• NM_052872.4:c.34-1809C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-52240759-G-A
• chr6-52240759-G-T

Variant summary

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

The NM_052872.4(IL17F):​c.34-1809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,692 control chromosomes in the GnomAD database, including 9,195 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 0.32 (9195 hom., cov: 30)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	NM_052872.4	c.34-1809C>T		intron_variant	Intron 1 of 2	ENST00000336123.5	NP_443104.1
IL17F	XM_011514276.1	c.34-1809C>T		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.34-1809C>T		intron_variant	Intron 1 of 2	1	NM_052872.4	ENSP00000337432.4
IL17F	ENST00000699946.1	c.34-1809C>T		intron_variant	Intron 2 of 3			ENSP00000514702.1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48999 AN: 151574 Hom.: 9199 Cov.: 30

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.323 AC: 48994 AN: 151692 Hom.: 9195 Cov.: 30 AF XY: 0.322 AC XY: 23882 AN XY: 74082

African (AFR) AF: 0.122 AC: 5043 AN: 41360

American (AMR) AF: 0.296 AC: 4509 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1803 AN: 5132

South Asian (SAS) AF: 0.411 AC: 1975 AN: 4808

European-Finnish (FIN) AF: 0.396 AC: 4147 AN: 10472

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28937 AN: 67920

Other (OTH) AF: 0.347 AC: 732 AN: 2110

Alfa AF: 0.388 Hom.: 20060

Bravo AF: 0.305

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.64
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs12203582; hg19: chr6-52105557;