Genetic Variant NM_052872.4:c.34-361G>T (chr6-52239311-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

Publications

7 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17F	NM_052872.4 link	c.34-361G>T		intron_variant	Intron 1 of 2	ENST00000336123.5	NP_443104.1	Q96PD4
IL17F	XM_011514276.1 link	c.34-361G>T		intron_variant	Intron 2 of 3		XP_011512578.1	Q96PD4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL17F	ENST00000336123.5 link	c.34-361G>T	intron_variant	Intron 1 of 2	1	NM_052872.4	ENSP00000337432.4	Q96PD4
IL17F	ENST00000699946.1 link	c.34-361G>T	intron_variant	Intron 2 of 3			ENSP00000514702.1	Q96PD4
IL17F	ENST00000478427.1 link	n.-144G>T	upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0665

AC:

10113

AN:

152056

Hom.:

392

Cov.:

show subpopulations

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

show subpopulations

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:

AN:

492

European-Non Finnish (NFE)

AF:

0.0435

AC:

2939

AN:

67576

Other (OTH)

AF:

0.0521

AC:

325

AN:

6234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

277

554

831

1108

1385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<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:

10118

AN:

152174

Hom.:

389

Cov.:

AF XY:

0.0700

AC XY:

5210

AN XY:

74400

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0485

AC:

3301

AN:

68008

Other (OTH)

AF:

0.0512

AC:

108

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

480

959

1439

1918

2398

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:

0.0522

Hom.:

423

Bravo

AF:

0.0612

Asia WGS

AF:

0.106

AC:

366

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.058

(source)

DANN

Benign

0.31

PhyloP100

-2.0

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over