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GeneBe

rs189013166

chr3-9933455-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_153460.4(IL17RC):c.2025G>A(p.Gly675=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00386 in 1,613,026 control chromosomes in the GnomAD database, including 122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 11 hom., cov: 34)
Exomes 𝑓: 0.0039 ( 111 hom. )

Consequence

IL17RC
NM_153460.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0180
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 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=-0.81).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-9933455-G-A is Benign according to our data. Variant chr3-9933455-G-A is described in ClinVar as [Benign]. Clinvar id is 475927.Status of the report is criteria_provided_single_submitter, 1 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=0.018 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0037 (564/152376) while in subpopulation SAS AF= 0.0472 (228/4832). AF 95% confidence interval is 0.0422. There are 11 homozygotes in gnomad4. There are 352 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL17RCNM_153460.4 linkuse as main transcriptc.2025G>A p.Gly675= synonymous_variant 19/19 ENST00000403601.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL17RCENST00000403601.8 linkuse as main transcriptc.2025G>A p.Gly675= synonymous_variant 19/191 NM_153460.4 P4Q8NAC3-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00369
AC:
562
AN:
152258
Hom.:
10
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0112
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0212
Gnomad SAS
AF:
0.0474
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00998
AC:
2414
AN:
241870
Hom.:
47
AF XY:
0.0109
AC XY:
1441
AN XY:
132754
show subpopulations
Gnomad AFR exome
AF:
0.000478
Gnomad AMR exome
AF:
0.0220
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0217
Gnomad SAS exome
AF:
0.0387
Gnomad FIN exome
AF:
0.000142
Gnomad NFE exome
AF:
0.000574
Gnomad OTH exome
AF:
0.00460
GnomAD4 exome
AF:
0.00387
AC:
5655
AN:
1460650
Hom.:
111
Cov.:
34
AF XY:
0.00483
AC XY:
3512
AN XY:
726618
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.0218
Gnomad4 ASJ exome
AF:
0.0000767
Gnomad4 EAS exome
AF:
0.0182
Gnomad4 SAS exome
AF:
0.0384
Gnomad4 FIN exome
AF:
0.000209
Gnomad4 NFE exome
AF:
0.000297
Gnomad4 OTH exome
AF:
0.00456
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00370
AC:
564
AN:
152376
Hom.:
11
Cov.:
34
AF XY:
0.00472
AC XY:
352
AN XY:
74516
show subpopulations
Gnomad4 AFR
AF:
0.000553
Gnomad4 AMR
AF:
0.0114
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0212
Gnomad4 SAS
AF:
0.0472
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.000857
Hom.:
0
Bravo
AF:
0.00369
Asia WGS
AF:
0.0220
AC:
77
AN:
3478
EpiCase
AF:
0.000654
EpiControl
AF:
0.000593

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 submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
4.3
Dann
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs189013166; hg19: chr3-9975139; API