rs140139879
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_014339.7(IL17RA):c.1338G>A(p.Leu446=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,608,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
IL17RA
NM_014339.7 synonymous
NM_014339.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.23
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 -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 22-17108557-G-A is Benign according to our data. Variant chr22-17108557-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 476360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.23 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000236 (36/152342) while in subpopulation AFR AF= 0.000649 (27/41594). AF 95% confidence interval is 0.000458. There are 0 homozygotes in gnomad4. There are 15 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.1338G>A | p.Leu446= | synonymous_variant | 13/13 | ENST00000319363.11 | NP_055154.3 | |
IL17RA | NM_001289905.2 | c.1236G>A | p.Leu412= | synonymous_variant | 12/12 | NP_001276834.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.1338G>A | p.Leu446= | synonymous_variant | 13/13 | 1 | NM_014339.7 | ENSP00000320936 | P2 | |
IL17RA | ENST00000612619.2 | c.1236G>A | p.Leu412= | synonymous_variant | 12/12 | 5 | ENSP00000479970 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000236 AC: 36AN: 152224Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000616 AC: 15AN: 243374Hom.: 0 AF XY: 0.0000377 AC XY: 5AN XY: 132488
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1455996Hom.: 0 Cov.: 62 AF XY: 0.00000690 AC XY: 5AN XY: 724570
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GnomAD4 genome AF: 0.000236 AC: 36AN: 152342Hom.: 0 Cov.: 34 AF XY: 0.000201 AC XY: 15AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency 51 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at