GeneBe

3-9917263-TGG-TGGGG

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000451271.5(IL17RC):​n.-45_-44dupGG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.014 ( 43 hom., cov: 0)
Exomes 𝑓: 0.0095 ( 6 hom. )

Consequence

IL17RC
ENST00000451271.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0890

Publications

1 publications found
Variant links:
Genes affected
IL17RC (HGNC:18358): (interleukin 17 receptor C) This gene encodes a single-pass type I membrane protein that shares similarity with the interleukin-17 receptor (IL-17RA). Unlike IL-17RA, which is predominantly expressed in hemopoietic cells, and binds with high affinity to only IL-17A, this protein is expressed in nonhemopoietic tissues, and binds both IL-17A and IL-17F with similar affinities. The proinflammatory cytokines, IL-17A and IL-17F, have been implicated in the progression of inflammatory and autoimmune diseases. Multiple alternatively spliced transcript variants encoding different isoforms have been detected for this gene, and it has been proposed that soluble, secreted proteins lacking transmembrane and intracellular domains may function as extracellular antagonists to cytokine signaling. [provided by RefSeq, Feb 2011]
IL17RC Gene-Disease associations (from GenCC):
  • chronic mucocutaneous candidiasis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • candidiasis, familial, 9
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0143 (2141/150056) while in subpopulation AFR AF = 0.0411 (1686/41062). AF 95% confidence interval is 0.0394. There are 43 homozygotes in GnomAd4. There are 1061 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
BS2
High AC in GnomAd4 at 2141 Unknown,AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL17RCNM_153460.4 linkc.-45_-44dupGG 5_prime_UTR_variant Exon 1 of 19 ENST00000403601.8 NP_703190.2 Q8NAC3-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000288550ENST00000683484.1 linkn.-45_-44dupGG non_coding_transcript_exon_variant Exon 1 of 24 ENSP00000507040.1 A0A804HIF2
IL17RCENST00000403601.8 linkc.-45_-44dupGG 5_prime_UTR_variant Exon 1 of 19 1 NM_153460.4 ENSP00000384969.3 Q8NAC3-2
ENSG00000288550ENST00000683484.1 linkn.-45_-44dupGG 5_prime_UTR_variant Exon 1 of 24 ENSP00000507040.1 A0A804HIF2

Frequencies

GnomAD3 genomes
AF:
0.0142
AC:
2131
AN:
149950
Hom.:
43
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0409
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0231
Gnomad ASJ
AF:
0.000292
Gnomad EAS
AF:
0.000791
Gnomad SAS
AF:
0.00191
Gnomad FIN
AF:
0.000783
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000953
Gnomad OTH
AF:
0.0106
GnomAD4 exome
AF:
0.00948
AC:
10660
AN:
1123906
Hom.:
6
Cov.:
20
AF XY:
0.00929
AC XY:
5195
AN XY:
558936
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0572
AC:
1333
AN:
23286
American (AMR)
AF:
0.0198
AC:
506
AN:
25568
Ashkenazi Jewish (ASJ)
AF:
0.00400
AC:
75
AN:
18762
East Asian (EAS)
AF:
0.000728
AC:
24
AN:
32970
South Asian (SAS)
AF:
0.00512
AC:
327
AN:
63840
European-Finnish (FIN)
AF:
0.00552
AC:
239
AN:
43322
Middle Eastern (MID)
AF:
0.00858
AC:
31
AN:
3614
European-Non Finnish (NFE)
AF:
0.00883
AC:
7644
AN:
866048
Other (OTH)
AF:
0.0103
AC:
481
AN:
46496
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.297
Heterozygous variant carriers
0
1024
2049
3073
4098
5122
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
358
716
1074
1432
1790
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0143
AC:
2141
AN:
150056
Hom.:
43
Cov.:
0
AF XY:
0.0145
AC XY:
1061
AN XY:
73236
show subpopulations
African (AFR)
AF:
0.0411
AC:
1686
AN:
41062
American (AMR)
AF:
0.0230
AC:
348
AN:
15154
Ashkenazi Jewish (ASJ)
AF:
0.000292
AC:
1
AN:
3430
East Asian (EAS)
AF:
0.000793
AC:
4
AN:
5042
South Asian (SAS)
AF:
0.00170
AC:
8
AN:
4700
European-Finnish (FIN)
AF:
0.000783
AC:
8
AN:
10222
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
0.000953
AC:
64
AN:
67170
Other (OTH)
AF:
0.0105
AC:
22
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
94
188
282
376
470
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
22
44
66
88
110
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000339
Hom.:
413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.089
Mutation Taster
=300/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs530330109; hg19: chr3-9958947; API