GeneBe

rs922730539

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014339.7(IL17RA):​c.-6C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

IL17RA
NM_014339.7 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

0 publications found
Variant links:
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]
IL17RA Gene-Disease associations (from GenCC):
  • immunodeficiency 51
    Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • chronic mucocutaneous candidiasis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL17RANM_014339.7 linkc.-6C>A 5_prime_UTR_variant Exon 1 of 13 ENST00000319363.11 NP_055154.3 Q96F46-1
IL17RANM_001289905.2 linkc.-6C>A 5_prime_UTR_variant Exon 1 of 12 NP_001276834.1 Q96F46-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL17RAENST00000319363.11 linkc.-6C>A 5_prime_UTR_variant Exon 1 of 13 1 NM_014339.7 ENSP00000320936.6 Q96F46-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
3460
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1165578
Hom.:
0
Cov.:
58
AF XY:
0.00
AC XY:
0
AN XY:
561608
African (AFR)
AF:
0.00
AC:
0
AN:
23418
American (AMR)
AF:
0.00
AC:
0
AN:
9026
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15784
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26898
South Asian (SAS)
AF:
0.00
AC:
0
AN:
44330
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
27312
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4726
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
966666
Other (OTH)
AF:
0.00
AC:
0
AN:
47418
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
5.0
DANN
Benign
0.71
PhyloP100
-1.5
PromoterAI
0.040
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs922730539; hg19: chr22-17565976; API