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GeneBe

22-17085084-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014339.7(IL17RA):c.-8G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,315,154 control chromosomes in the GnomAD database, including 430,895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 53550 hom., cov: 34)
Exomes 𝑓: 0.80 ( 377345 hom. )

Consequence

IL17RA
NM_014339.7 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.04
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]

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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=-0.86).
BP6
Variant 22-17085084-G-C is Benign according to our data. Variant chr22-17085084-G-C is described in ClinVar as [Benign]. Clinvar id is 340561.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-17085084-G-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL17RANM_014339.7 linkuse as main transcriptc.-8G>C 5_prime_UTR_variant 1/13 ENST00000319363.11
IL17RANM_001289905.2 linkuse as main transcriptc.-8G>C 5_prime_UTR_variant 1/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL17RAENST00000319363.11 linkuse as main transcriptc.-8G>C 5_prime_UTR_variant 1/131 NM_014339.7 P2Q96F46-1

Frequencies

GnomAD3 genomes
AF:
0.833
AC:
126564
AN:
152026
Hom.:
53500
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.960
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.659
Gnomad ASJ
AF:
0.811
Gnomad EAS
AF:
0.606
Gnomad SAS
AF:
0.764
Gnomad FIN
AF:
0.842
Gnomad MID
AF:
0.927
Gnomad NFE
AF:
0.815
Gnomad OTH
AF:
0.818
GnomAD3 exomes
AF:
0.804
AC:
2525
AN:
3142
Hom.:
1034
AF XY:
0.802
AC XY:
1585
AN XY:
1976
show subpopulations
Gnomad AFR exome
AF:
0.974
Gnomad AMR exome
AF:
0.676
Gnomad ASJ exome
AF:
0.865
Gnomad EAS exome
AF:
0.713
Gnomad SAS exome
AF:
0.786
Gnomad FIN exome
AF:
0.859
Gnomad NFE exome
AF:
0.818
Gnomad OTH exome
AF:
0.810
GnomAD4 exome
AF:
0.804
AC:
935247
AN:
1163018
Hom.:
377345
Cov.:
52
AF XY:
0.804
AC XY:
450580
AN XY:
560162
show subpopulations
Gnomad4 AFR exome
AF:
0.969
Gnomad4 AMR exome
AF:
0.599
Gnomad4 ASJ exome
AF:
0.819
Gnomad4 EAS exome
AF:
0.607
Gnomad4 SAS exome
AF:
0.795
Gnomad4 FIN exome
AF:
0.833
Gnomad4 NFE exome
AF:
0.807
Gnomad4 OTH exome
AF:
0.800
GnomAD4 genome
AF:
0.833
AC:
126662
AN:
152136
Hom.:
53550
Cov.:
34
AF XY:
0.829
AC XY:
61676
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.960
Gnomad4 AMR
AF:
0.658
Gnomad4 ASJ
AF:
0.811
Gnomad4 EAS
AF:
0.606
Gnomad4 SAS
AF:
0.765
Gnomad4 FIN
AF:
0.842
Gnomad4 NFE
AF:
0.815
Gnomad4 OTH
AF:
0.817
Alfa
AF:
0.834
Hom.:
6620
Bravo
AF:
0.821
Asia WGS
AF:
0.681
AC:
2360
AN:
3470

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:2
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 29, 2016Variant 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 -
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJan 24, 2024This variant is classified as Benign based on local population frequency. This variant was detected in 91% of patients studied by a panel of primary immunodeficiencies. Number of patients: 86. Only high quality variants are reported. -
Familial Candidiasis, Recessive Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Immunodeficiency 51 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabAug 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
9.0
Dann
Benign
0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs917865; hg19: chr22-17565974; API