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rs763780

Variant summary

Our verdict is Benign. Variant got -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. 12/19 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

1
17

Clinical Significance

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

Conservation

PhyloP100: 0.761
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 357466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-52236941-T-C is described in Lovd as [Benign].
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/exons MANE UniProt
IL17FNM_052872.4 linkuse as main transcriptc.482A>G p.His161Arg missense_variant 3/3 ENST00000336123.5
IL17FXM_011514276.1 linkuse as main transcriptc.482A>G p.His161Arg missense_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL17FENST00000336123.5 linkuse as main transcriptc.482A>G p.His161Arg missense_variant 3/31 NM_052872.4 P1
IL17FENST00000478427.1 linkuse as main transcriptn.666A>G non_coding_transcript_exon_variant 2/21
IL17FENST00000699946.1 linkuse as main transcriptc.482A>G p.His161Arg missense_variant 4/4 P1

Frequencies

GnomAD3 genomes
AF:
0.0665
AC:
10118
AN:
152120
Hom.:
393
Cov.:
32
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
GnomAD3 exomes
AF:
0.0672
AC:
16859
AN:
250950
Hom.:
667
AF XY:
0.0676
AC XY:
9174
AN XY:
135628
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 SAS exome
AF:
0.0739
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.:
30
AF XY:
0.0551
AC XY:
40067
AN XY:
726828
show subpopulations
Gnomad4 AFR exome
AF:
0.0839
Gnomad4 AMR exome
AF:
0.0453
Gnomad4 ASJ exome
AF:
0.0421
Gnomad4 EAS exome
AF:
0.130
Gnomad4 SAS exome
AF:
0.0714
Gnomad4 FIN exome
AF:
0.103
Gnomad4 NFE exome
AF:
0.0480
Gnomad4 OTH exome
AF:
0.0616
GnomAD4 genome
AF:
0.0665
AC:
10123
AN:
152238
Hom.:
390
Cov.:
32
AF XY:
0.0701
AC XY:
5214
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0830
Gnomad4 AMR
AF:
0.0484
Gnomad4 ASJ
AF:
0.0493
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.0770
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.0484
Gnomad4 OTH
AF:
0.0520
Alfa
AF:
0.0508
Hom.:
478
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

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Candidiasis, familial, 6 Benign:2
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaMar 06, 2018This 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. -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018This variant is associated with the following publications: (PMID: 22812194, 24164796, 31616423, 31831764, 20620187, 24440568, 16630936, 20618772, 24829928, 22579472, 21615796) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.090
BayesDel_addAF
Benign
-0.79
T
BayesDel_noAF
Benign
-0.77
Cadd
Benign
4.2
Dann
Benign
0.60
DEOGEN2
Benign
0.27
T
Eigen
Benign
-0.94
Eigen_PC
Benign
-0.94
FATHMM_MKL
Benign
0.061
N
LIST_S2
Benign
0.42
T
MetaRNN
Benign
0.0019
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.6
L
MutationTaster
Benign
1.0
P
PrimateAI
Benign
0.36
T
PROVEAN
Uncertain
-2.6
D
REVEL
Benign
0.066
Sift
Benign
0.19
T
Sift4G
Benign
0.13
T
Polyphen
0.048
B
Vest4
0.010
MPC
0.13
ClinPred
0.0043
T
GERP RS
2.8
Varity_R
0.32
gMVP
0.56

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs763780; hg19: chr6-52101739; COSMIC: COSV60233806; API