rs879575
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_014339.7(IL17RA):c.1458C>T(p.Ile486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,607,998 control chromosomes in the GnomAD database, including 41,505 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.20 ( 3323 hom., cov: 34)
Exomes 𝑓: 0.22 ( 38182 hom. )
Consequence
IL17RA
NM_014339.7 synonymous
NM_014339.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.98
Genes affected
IL17RA (HGNC:5985): (interleukin 17 receptor A) Interleukin 17A (IL17A) is a proinflammatory cytokine secreted by activated T-lymphocytes. It is a potent inducer of the maturation of CD34-positive hematopoietic precursors into neutrophils. The transmembrane protein encoded by this gene (interleukin 17A receptor; IL17RA) is a ubiquitous type I membrane glycoprotein that binds with low affinity to interleukin 17A. Interleukin 17A and its receptor play a pathogenic role in many inflammatory and autoimmune diseases such as rheumatoid arthritis. Like other cytokine receptors, this receptor likely has a multimeric structure. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 22-17108677-C-T is Benign according to our data. Variant chr22-17108677-C-T is described in ClinVar as [Benign]. Clinvar id is 340598.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-17108677-C-T is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=1.98 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.1458C>T | p.Ile486= | synonymous_variant | 13/13 | ENST00000319363.11 | |
IL17RA | NM_001289905.2 | c.1356C>T | p.Ile452= | synonymous_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.1458C>T | p.Ile486= | synonymous_variant | 13/13 | 1 | NM_014339.7 | P2 | |
IL17RA | ENST00000612619.2 | c.1356C>T | p.Ile452= | synonymous_variant | 12/12 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.204 AC: 31020AN: 152148Hom.: 3324 Cov.: 34
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GnomAD3 exomes AF: 0.193 AC: 47167AN: 244674Hom.: 5055 AF XY: 0.197 AC XY: 26216AN XY: 133032
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GnomAD4 exome AF: 0.224 AC: 326044AN: 1455732Hom.: 38182 Cov.: 62 AF XY: 0.223 AC XY: 161699AN XY: 724526
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GnomAD4 genome AF: 0.204 AC: 31028AN: 152266Hom.: 3323 Cov.: 34 AF XY: 0.201 AC XY: 14966AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:4Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 28% of patients studied by a panel of primary immunodeficiencies. Number of patients: 27. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Familial Candidiasis, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Immunodeficiency 51 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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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