6-52236808-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_052872.4(IL17F):c.*123C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00974 in 798,730 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 9 hom., cov: 32)
Exomes 𝑓: 0.010 ( 46 hom. )
Consequence
IL17F
NM_052872.4 3_prime_UTR
NM_052872.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.454
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 6-52236808-G-A is Benign according to our data. Variant chr6-52236808-G-A is described in ClinVar as [Benign]. Clinvar id is 357465.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 1280 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL17F | NM_052872.4 | c.*123C>T | 3_prime_UTR_variant | 3/3 | ENST00000336123.5 | NP_443104.1 | ||
IL17F | XM_011514276.1 | c.*123C>T | 3_prime_UTR_variant | 4/4 | XP_011512578.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17F | ENST00000336123.5 | c.*123C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_052872.4 | ENSP00000337432 | P1 | ||
IL17F | ENST00000478427.1 | n.799C>T | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
IL17F | ENST00000699946.1 | c.*123C>T | 3_prime_UTR_variant | 4/4 | ENSP00000514702 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00841 AC: 1279AN: 152118Hom.: 9 Cov.: 32
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GnomAD4 exome AF: 0.0100 AC: 6497AN: 646494Hom.: 46 Cov.: 7 AF XY: 0.00975 AC XY: 3418AN XY: 350570
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GnomAD4 genome AF: 0.00841 AC: 1280AN: 152236Hom.: 9 Cov.: 32 AF XY: 0.00824 AC XY: 613AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Candidiasis, familial, 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at