3-9928347-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153460.4(IL17RC):c.920A>G(p.Gln307Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,603,840 control chromosomes in the GnomAD database, including 792,850 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 1.0 ( 75524 hom., cov: 34)

Exomes 𝑓: 0.99 ( 717326 hom. )

Consequence

IL17RC
NM_153460.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.08

Publications

28 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)

IL17RC links:

ENSG00000288550 (HGNC:):

ENSG00000288550 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.66898E-7).

BP6

Variant 3-9928347-A-G is Benign according to our data. Variant chr3-9928347-A-G is described in ClinVar as Benign. ClinVar VariationId is 1164863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RC	NM_153460.4 link	c.920A>G	p.Gln307Arg	missense_variant	Exon 11 of 19	ENST00000403601.8	NP_703190.2	Q8NAC3-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RC	ENST00000403601.8 link	c.920A>G	p.Gln307Arg	missense_variant	Exon 11 of 19	1	NM_153460.4	ENSP00000384969.3		Q8NAC3-2
ENSG00000288550	ENST00000683484.1 link	n.836A>G		non_coding_transcript_exon_variant	Exon 10 of 24			ENSP00000507040.1		A0A804HIF2

Frequencies

GnomAD3 genomes

AF:

0.996

AC:

151585

AN:

152242

Hom.:

75465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.998

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.995

Gnomad ASJ

AF:

0.993

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.993

Gnomad OTH

AF:

0.994

GnomAD2 exomes

AF:

0.995

AC:

245455

AN:

246602

AF XY:

0.995

show subpopulations

Gnomad AFR exome

AF:

0.999

Gnomad AMR exome

AF:

0.995

Gnomad ASJ exome

AF:

0.995

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.999

Gnomad NFE exome

AF:

0.993

Gnomad OTH exome

AF:

0.996

GnomAD4 exome

AF:

0.994

AC:

1443034

AN:

1451480

Hom.:

717326

Cov.:

AF XY:

0.994

AC XY:

716275

AN XY:

720402

show subpopulations

African (AFR)

AF:

0.999

AC:

33169

AN:

33210

American (AMR)

AF:

0.995

AC:

43847

AN:

44064

Ashkenazi Jewish (ASJ)

AF:

0.994

AC:

25584

AN:

25748

East Asian (EAS)

AF:

1.00

AC:

39464

AN:

39464

South Asian (SAS)

AF:

0.998

AC:

85508

AN:

85668

European-Finnish (FIN)

AF:

0.999

AC:

52677

AN:

52726

Middle Eastern (MID)

AF:

0.994

AC:

5688

AN:

5720

European-Non Finnish (NFE)

AF:

0.993

AC:

1097511

AN:

1104982

Other (OTH)

AF:

0.995

AC:

59586

AN:

59898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

489

979

1468

1958

2447

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21664

43328

64992

86656

108320

<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:

0.996

AC:

151703

AN:

152360

Hom.:

75524

Cov.:

AF XY:

0.996

AC XY:

74196

AN XY:

74494

show subpopulations

African (AFR)

AF:

0.998

AC:

41516

AN:

41580

American (AMR)

AF:

0.995

AC:

15243

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.993

AC:

3448

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5166

AN:

5166

South Asian (SAS)

AF:

0.999

AC:

4829

AN:

4832

European-Finnish (FIN)

AF:

1.00

AC:

10627

AN:

10632

Middle Eastern (MID)

AF:

1.00

AC:

294

AN:

294

European-Non Finnish (NFE)

AF:

0.993

AC:

67564

AN:

68042

Other (OTH)

AF:

0.994

AC:

2104

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

114

152

190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

916

1832

2748

3664

4580

<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:

0.994

Hom.:

95461

Bravo

AF:

0.995

TwinsUK

AF:

0.996

AC:

3692

ALSPAC

AF:

0.994

AC:

3829

ESP6500AA

AF:

0.999

AC:

4401

ESP6500EA

AF:

0.994

AC:

8543

ExAC

AF:

0.996

AC:

120744

Asia WGS

AF:

1.00

AC:

3478

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Candidiasis, familial, 9

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 19, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 95. Only high quality variants are reported. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.88

(source)

DANN

Benign

0.097

DEOGEN2

Benign

0.023

.;.;.;T;.;.;.;.;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.12

T;.;T;T;T;T;T;T;T

MetaRNN

Benign

6.7e-7

T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-0.95

.;.;.;N;.;.;.;.;.

PhyloP100

-1.1

PrimateAI

Benign

0.27

PROVEAN

Benign

0.0

.;N;N;N;.;N;N;N;N

REVEL

Benign

0.010

Sift

Benign

1.0

.;T;T;T;.;T;T;T;T

Sift4G

Benign

1.0

T;T;T;T;.;T;T;T;T

Polyphen

0.0

.;B;.;B;B;.;B;.;.

Vest4

0.047

MPC

0.25

ClinPred

0.0021

GERP RS

1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.038

gMVP

0.31

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over