rs763780
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_052872(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 0.0665 in 152120 control chromosomes in the gnomAD Genomes database, including 393 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 (β β ).
Frequency
Genomes: π 0.067 ( 393 hom., cov: 32)
Exomes π: 0.067 ( 667 hom. )
Consequence
IL17F
NM_052872 missense
NM_052872 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 0.761
Links
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
?
GnomAd 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 |
---|---|---|---|---|---|---|---|
IL17F | NM_052872.4 | c.482A>G | p.His161Arg | missense_variant | 3/3 | ENST00000336123.5 | |
IL17F | XM_011514276.1 | c.482A>G | p.His161Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17F | ENST00000336123.5 | c.482A>G | p.His161Arg | missense_variant | 3/3 | 1 | NM_052872.4 | P1 | |
IL17F | ENST00000478427.1 | n.666A>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
IL17F | ENST00000699946.1 | c.482A>G | p.His161Arg | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0665 AC: 10118AN: 152120Hom.: 393 Cov.: 32
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32
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GnomAD3 exomes AF: 0.0672 AC: 16859AN: 250950Hom.: 667 AF XY: 0.0676 AC XY: 9174AN XY: 135628
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GnomAD4 exome AF: 0.0548 AC: 80034AN: 1460808Hom.: 2607 AF XY: 0.0551 AC XY: 40067AN XY: 726828
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146
ALSPAC
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205
ESP6500AA
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395
ESP6500EA
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425
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8112
Asia WGS
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372
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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 submitter | clinical testing | Invitae | Nov 03, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 22812194, 24164796, 31616423, 31831764, 20620187, 24440568, 16630936, 20618772, 24829928, 22579472, 21615796) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at