rs7771466

Variant names:

• chr6-52239311-C-A
• rs7771466
• NM_052872.4:c.34-361G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-52239311-C-A
• chr6-52239311-C-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.34-361G>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
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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.34-361G>T		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.34-361G>T		intron	N/A	ENSP00000337432.4	Q96PD4
	IL17F	ENST00000699946.1		c.34-361G>T		intron	N/A	ENSP00000514702.1	Q96PD4
	IL17F	ENST00000478427.1	TSL:1	n.-144G>T		upstream_gene	N/A

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

African (AFR) AF: 0.0747 AC: 326 AN: 4366

American (AMR) AF: 0.0408 AC: 216 AN: 5292

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 126 AN: 3162

East Asian (EAS) AF: 0.132 AC: 903 AN: 6820

South Asian (SAS) AF: 0.0615 AC: 826 AN: 13434

European-Finnish (FIN) AF: 0.0841 AC: 389 AN: 4626

Middle Eastern (MID) AF: 0.0366 AC: 18 AN: 492

European-Non Finnish (NFE) AF: 0.0435 AC: 2939 AN: 67576

Other (OTH) AF: 0.0521 AC: 325 AN: 6234

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

African (AFR) AF: 0.0827 AC: 3431 AN: 41504

American (AMR) AF: 0.0484 AC: 741 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.147 AC: 763 AN: 5184

South Asian (SAS) AF: 0.0768 AC: 370 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10576

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3301 AN: 68008

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0522 Hom.: 423

Bravo AF: 0.0612

Asia WGS AF: 0.106 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.058
DANN	Benign	0.31
PhyloP100		-2.0
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: rs7771466;

hg19: chr6-52104109;