rs139727834
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_153460.4(IL17RC):c.591C>G(p.Leu197Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,453,174 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 (★). Synonymous variant affecting the same amino acid position (i.e. L197L) has been classified as Benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
IL17RC
NM_153460.4 synonymous
NM_153460.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.09
Publications
0 publications found
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 candidiasisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- candidiasis, familial, 9Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 3-9920938-C-G is Benign according to our data. Variant chr3-9920938-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 1988831.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-5.09 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| IL17RC | ENST00000403601.8 | c.591C>G | p.Leu197Leu | synonymous_variant | Exon 7 of 19 | 1 | NM_153460.4 | ENSP00000384969.3 | ||
| ENSG00000288550 | ENST00000683484.1 | n.577+336C>G | intron_variant | Intron 6 of 23 | ENSP00000507040.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1453174Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 722814 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1453174
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
722814
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32980
American (AMR)
AF:
AC:
0
AN:
42512
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25598
East Asian (EAS)
AF:
AC:
0
AN:
39506
South Asian (SAS)
AF:
AC:
0
AN:
84490
European-Finnish (FIN)
AF:
AC:
0
AN:
53220
Middle Eastern (MID)
AF:
AC:
0
AN:
5626
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1109248
Other (OTH)
AF:
AC:
0
AN:
59994
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
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2
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0.00
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0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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<30
30-35
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Candidiasis, familial, 9 Benign:1
Jul 14, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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