rs763780

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.482A>G(p.His161Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0559 in 1,613,046 control chromosomes in the GnomAD database, including 2,997 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. H161H) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.066 ( 390 hom., cov: 32)

Exomes 𝑓: 0.055 ( 2607 hom. )

Consequence

IL17F
NM_052872.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.761

Publications

417 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=0.0018661618).

BP6

Variant 6-52236941-T-C is Benign according to our data. Variant chr6-52236941-T-C is described in ClinVar as Benign. ClinVar VariationId is 357466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17F	NM_052872.4	MANE Select	c.482A>G	p.His161Arg	missense	Exon 3 of 3	NP_443104.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
IL17F	ENST00000336123.5	TSL:1 MANE Select	c.482A>G	p.His161Arg	missense	Exon 3 of 3	ENSP00000337432.4
IL17F	ENST00000478427.1	TSL:1	n.666A>G		non_coding_transcript_exon	Exon 2 of 2
IL17F	ENST00000699946.1		c.482A>G	p.His161Arg	missense	Exon 4 of 4	ENSP00000514702.1

Frequencies

GnomAD3 genomes

AF:

0.0665

AC:

10118

AN:

152120

Hom.:

393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0483

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.0773

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0484

Gnomad OTH

AF:

0.0526

GnomAD2 exomes

AF:

0.0672

AC:

16859

AN:

250950

AF XY:

0.0676

show subpopulations

Gnomad AFR exome

AF:

0.0868

Gnomad AMR exome

AF:

0.0451

Gnomad ASJ exome

AF:

0.0449

Gnomad EAS exome

AF:

0.149

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.0504

Gnomad OTH exome

AF:

0.0556

GnomAD4 exome

AF:

0.0548

AC:

80034

AN:

1460808

Hom.:

2607

Cov.:

AF XY:

0.0551

AC XY:

40067

AN XY:

726828

show subpopulations

African (AFR)

AF:

0.0839

AC:

2809

AN:

33464

American (AMR)

AF:

0.0453

AC:

2027

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0421

AC:

1100

AN:

26128

East Asian (EAS)

AF:

0.130

AC:

5145

AN:

39694

South Asian (SAS)

AF:

0.0714

AC:

6160

AN:

86232

European-Finnish (FIN)

AF:

0.103

AC:

5515

AN:

53408

Middle Eastern (MID)

AF:

0.0436

AC:

251

AN:

5762

European-Non Finnish (NFE)

AF:

0.0480

AC:

53307

AN:

1111030

Other (OTH)

AF:

0.0616

AC:

3720

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

3843

7686

11528

15371

19214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2090

4180

6270

8360

10450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0665

AC:

10123

AN:

152238

Hom.:

390

Cov.:

AF XY:

0.0701

AC XY:

5214

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0830

AC:

3449

AN:

41538

American (AMR)

AF:

0.0484

AC:

740

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3468

East Asian (EAS)

AF:

0.148

AC:

765

AN:

5180

South Asian (SAS)

AF:

0.0770

AC:

371

AN:

4820

European-Finnish (FIN)

AF:

0.113

AC:

1200

AN:

10616

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0484

AC:

3291

AN:

68012

Other (OTH)

AF:

0.0520

AC:

110

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

481

961

1442

1922

2403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0534

Hom.:

1095

Bravo

AF:

0.0612

TwinsUK

AF:

0.0394

AC:

146

ALSPAC

AF:

0.0532

AC:

205

ESP6500AA

AF:

0.0897

AC:

395

ESP6500EA

AF:

0.0494

AC:

425

ExAC

AF:

0.0668

AC:

8112

Asia WGS

AF:

0.107

AC:

372

AN:

3478

EpiCase

AF:

0.0450

EpiControl

AF:

0.0462

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Candidiasis, familial, 6 (2)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.2

(source)

DANN

Benign

0.60

DEOGEN2

Benign

0.27

Eigen

Benign

-0.94

Eigen_PC

Benign

-0.94

FATHMM_MKL

Benign

0.061

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.6

PhyloP100

0.76

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-2.6

REVEL

Benign

0.066

Sift

Benign

0.19

Sift4G

Benign

0.13

Polyphen

0.048

Vest4

0.010

MPC

0.13

ClinPred

0.0043

GERP RS

2.8

Varity_R

0.32

gMVP

0.56

Mutation Taster

=97/3

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over