rs17205308
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014339.7(IL17RA):c.551-9G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00597 in 1,614,086 control chromosomes in the GnomAD database, including 301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0098 ( 43 hom., cov: 32)
Exomes 𝑓: 0.0056 ( 258 hom. )
Consequence
IL17RA
NM_014339.7 splice_polypyrimidine_tract, intron
NM_014339.7 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00003007
2
Clinical Significance
Conservation
PhyloP100: -0.203
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 22-17101987-G-T is Benign according to our data. Variant chr22-17101987-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 340574.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.551-9G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000319363.11 | |||
IL17RA | NM_001289905.2 | c.551-9G>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.551-9G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014339.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00978 AC: 1487AN: 152088Hom.: 42 Cov.: 32
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GnomAD3 exomes AF: 0.0151 AC: 3792AN: 251458Hom.: 125 AF XY: 0.0134 AC XY: 1822AN XY: 135920
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GnomAD4 exome AF: 0.00558 AC: 8154AN: 1461880Hom.: 258 Cov.: 33 AF XY: 0.00546 AC XY: 3973AN XY: 727242
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GnomAD4 genome ? AF: 0.00978 AC: 1489AN: 152206Hom.: 43 Cov.: 32 AF XY: 0.0110 AC XY: 816AN XY: 74416
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Familial Candidiasis, Recessive Benign:1
Likely 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 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 31
Find out detailed SpliceAI scores and Pangolin per-transcript scores at