NM_052872.4:c.254+368C>G

Variant names:

• chr6-52238362-G-C
• rs612242
• NM_052872.4:c.254+368C>G

Variant summary

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

The NM_052872.4(IL17F):​c.254+368C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,208 control chromosomes in the GnomAD database, including 3,434 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 0.12 (3434 hom., cov: 33)
• Consequence: IL17F NM_052872.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 2 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)

LOC124901328 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052872.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17F	NM_052872.4	MANE Select	c.254+368C>G		intron	N/A	NP_443104.1	Q96PD4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17F	ENST00000336123.5	TSL:1 MANE Select	c.254+368C>G		intron	N/A	ENSP00000337432.4	Q96PD4
	IL17F	ENST00000478427.1	TSL:1	n.438+368C>G		intron	N/A
	IL17F	ENST00000699946.1		c.254+368C>G		intron	N/A	ENSP00000514702.1	Q96PD4

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18958 AN: 152090 Hom.: 3420 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00954

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.125 AC: 19018 AN: 152208 Hom.: 3434 Cov.: 33 AF XY: 0.121 AC XY: 9031 AN XY: 74426

African (AFR) AF: 0.404 AC: 16748 AN: 41474

American (AMR) AF: 0.0551 AC: 842 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.0330 AC: 171 AN: 5186

South Asian (SAS) AF: 0.0387 AC: 187 AN: 4826

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00953 AC: 648 AN: 68028

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.0767 Hom.: 265

Bravo AF: 0.141

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs612242;

hg19: chr6-52103160;