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GeneBe

3-9917349-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_153460.4(IL17RC):c.34C>T(p.Leu12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0046 in 1,614,114 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 133 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 130 hom. )

Consequence

IL17RC
NM_153460.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.438
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-9917349-C-T is Benign according to our data. Variant chr3-9917349-C-T is described in ClinVar as [Benign]. Clinvar id is 542534.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.438 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL17RCNM_153460.4 linkuse as main transcriptc.34C>T p.Leu12= synonymous_variant 1/19 ENST00000403601.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL17RCENST00000403601.8 linkuse as main transcriptc.34C>T p.Leu12= synonymous_variant 1/191 NM_153460.4 P4Q8NAC3-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0233
AC:
3545
AN:
152176
Hom.:
132
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0807
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00628
Gnomad ASJ
AF:
0.0112
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.0210
GnomAD3 exomes
AF:
0.00676
AC:
1696
AN:
250916
Hom.:
51
AF XY:
0.00510
AC XY:
692
AN XY:
135742
show subpopulations
Gnomad AFR exome
AF:
0.0893
Gnomad AMR exome
AF:
0.00307
Gnomad ASJ exome
AF:
0.00874
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000318
Gnomad OTH exome
AF:
0.00343
GnomAD4 exome
AF:
0.00265
AC:
3879
AN:
1461820
Hom.:
130
Cov.:
34
AF XY:
0.00234
AC XY:
1705
AN XY:
727210
show subpopulations
Gnomad4 AFR exome
AF:
0.0862
Gnomad4 AMR exome
AF:
0.00376
Gnomad4 ASJ exome
AF:
0.00945
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000147
Gnomad4 OTH exome
AF:
0.00633
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0233
AC:
3549
AN:
152294
Hom.:
133
Cov.:
32
AF XY:
0.0221
AC XY:
1645
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0805
Gnomad4 AMR
AF:
0.00627
Gnomad4 ASJ
AF:
0.0112
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.0208
Alfa
AF:
0.00471
Hom.:
39
Bravo
AF:
0.0271
Asia WGS
AF:
0.00318
AC:
11
AN:
3478
EpiCase
AF:
0.000382
EpiControl
AF:
0.000237

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

IL17RC-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 08, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Candidiasis, familial, 9 Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 29, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
15
Dann
Benign
0.77

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: rs7643547; hg19: chr3-9959033; API