rs115461448
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153460.4(IL17RC):c.970G>A(p.Ala324Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0141 in 1,604,258 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 21 hom., cov: 33)
Exomes 𝑓: 0.014 ( 184 hom. )
Consequence
IL17RC
NM_153460.4 missense
NM_153460.4 missense
Scores
2
12
Clinical Significance
Conservation
PhyloP100: 3.71
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0069948733).
BP6
?
Variant 3-9928397-G-A is Benign according to our data. Variant chr3-9928397-G-A is described in ClinVar as [Benign]. Clinvar id is 475918.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0118 (1805/152378) while in subpopulation SAS AF= 0.0184 (89/4832). AF 95% confidence interval is 0.0153. There are 21 homozygotes in gnomad4. There are 931 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 21 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RC | NM_153460.4 | c.970G>A | p.Ala324Thr | missense_variant | 11/19 | ENST00000403601.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RC | ENST00000403601.8 | c.970G>A | p.Ala324Thr | missense_variant | 11/19 | 1 | NM_153460.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1799AN: 152260Hom.: 19 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0121 AC: 2921AN: 241526Hom.: 28 AF XY: 0.0125 AC XY: 1643AN XY: 131710
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GnomAD4 exome AF: 0.0144 AC: 20891AN: 1451880Hom.: 184 Cov.: 41 AF XY: 0.0144 AC XY: 10428AN XY: 721828
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GnomAD4 genome ? AF: 0.0118 AC: 1805AN: 152378Hom.: 21 Cov.: 33 AF XY: 0.0125 AC XY: 931AN XY: 74516
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55
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71
ESP6500AA
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25
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148
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?
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1392
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Candidiasis, familial, 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;.;T;T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Uncertain
T
REVEL
Benign
Sift4G
Benign
T;T;T;T;.;T;T;T;T
Polyphen
0.70, 1.0, 0.51
.;P;.;D;P;.;P;.;.
Vest4
MPC
0.44
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at