6-52236960-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_052872.4(IL17F):c.463G>A(p.Val155Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0427 in 1,613,836 control chromosomes in the GnomAD database, including 1,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V155G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.030 ( 107 hom., cov: 32)

Exomes 𝑓: 0.044 ( 1663 hom. )

Consequence

IL17F
NM_052872.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: 5.34

Publications

36 publications found

Variant links:

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)

IL17F links:

LOC124901328 (HGNC:):

LOC124901328 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039727986).

BP6

Variant 6-52236960-C-T is Benign according to our data. Variant chr6-52236960-C-T is described in ClinVar as [Benign]. Clinvar id is 357468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	NM_052872.4 link	c.463G>A	p.Val155Ile	missense_variant	Exon 3 of 3	ENST00000336123.5	NP_443104.1	Q96PD4
IL17F	XM_011514276.1 link	c.463G>A	p.Val155Ile	missense_variant	Exon 4 of 4		XP_011512578.1	Q96PD4
LOC124901328	XR_007059607.1 link	n.-126C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL17F	ENST00000336123.5 link	c.463G>A	p.Val155Ile	missense_variant	Exon 3 of 3	1	NM_052872.4	ENSP00000337432.4	Q96PD4
IL17F	ENST00000478427.1 link	n.647G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
IL17F	ENST00000699946.1 link	c.463G>A	p.Val155Ile	missense_variant	Exon 4 of 4			ENSP00000514702.1	Q96PD4

Frequencies

GnomAD3 genomes

AF:

0.0303

AC:

4608

AN:

152104

Hom.:

107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00833

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.00346

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.0510

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0461

Gnomad OTH

AF:

0.0292

GnomAD2 exomes

AF:

0.0304

AC:

7630

AN:

251040

AF XY:

0.0307

show subpopulations

Gnomad AFR exome

AF:

0.00640

Gnomad AMR exome

AF:

0.0143

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.00207

Gnomad FIN exome

AF:

0.0504

Gnomad NFE exome

AF:

0.0454

Gnomad OTH exome

AF:

0.0347

GnomAD4 exome

AF:

0.0440

AC:

64248

AN:

1461614

Hom.:

1663

Cov.:

AF XY:

0.0431

AC XY:

31310

AN XY:

727144

show subpopulations

African (AFR)

AF:

0.00651

AC:

218

AN:

33478

American (AMR)

AF:

0.0152

AC:

678

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0125

AC:

328

AN:

26136

East Asian (EAS)

AF:

0.00731

AC:

290

AN:

39698

South Asian (SAS)

AF:

0.0151

AC:

1304

AN:

86254

European-Finnish (FIN)

AF:

0.0514

AC:

2746

AN:

53416

Middle Eastern (MID)

AF:

0.0111

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.0505

AC:

56166

AN:

1111764

Other (OTH)

AF:

0.0406

AC:

2454

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

3108

6217

9325

12434

15542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0303

AC:

4605

AN:

152222

Hom.:

107

Cov.:

AF XY:

0.0291

AC XY:

2167

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.00831

AC:

345

AN:

41526

American (AMR)

AF:

0.0201

AC:

308

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00979

AC:

AN:

3472

East Asian (EAS)

AF:

0.00347

AC:

AN:

5190

South Asian (SAS)

AF:

0.0133

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0510

AC:

541

AN:

10602

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0461

AC:

3136

AN:

68000

Other (OTH)

AF:

0.0284

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

242

483

725

966

1208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0389

Hom.:

427

Bravo

AF:

0.0268

TwinsUK

AF:

0.0510

AC:

189

ALSPAC

AF:

0.0415

AC:

160

ESP6500AA

AF:

0.00908

AC:

ESP6500EA

AF:

0.0440

AC:

378

ExAC

AF:

0.0304

AC:

3692

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.0384

EpiControl

AF:

0.0413

ClinVar

Significance: Benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Candidiasis, familial, 6

Benign:2

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1Other:1

Jun 09, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

IL17F-related disorder

Benign:1

Sep 25, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.36

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.19

Eigen

Uncertain

0.61

Eigen_PC

Uncertain

0.60

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.83

MetaRNN

Benign

0.0040

MetaSVM

Benign

-0.57

MutationAssessor

Uncertain

2.3

PhyloP100

5.3

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.93

REVEL

Benign

0.18

Sift

Uncertain

0.024

Sift4G

Benign

0.085

Polyphen

0.99

Vest4

0.13

MPC

0.40

ClinPred

0.015

GERP RS

5.7

Varity_R

0.64

gMVP

0.71

Mutation Taster

=81/19

polymorphism (auto)

(source)

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

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6-52236960-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over