rs115461448

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

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

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.71

Publications

10 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=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 VariationId is 475918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High AC in GnomAd4 at 1805 Unknown,AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RC	NM_153460.4 link	c.970G>A	p.Ala324Thr	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.970G>A	p.Ala324Thr	missense_variant	Exon 11 of 19	1	NM_153460.4	ENSP00000384969.3		Q8NAC3-2
ENSG00000288550	ENST00000683484.1 link	n.886G>A		non_coding_transcript_exon_variant	Exon 10 of 24			ENSP00000507040.1		A0A804HIF2

Frequencies

GnomAD3 genomes

AF:

0.0118

AC:

1799

AN:

152260

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00463

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0165

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0184

Gnomad FIN

AF:

0.0120

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0156

Gnomad OTH

AF:

0.0148

GnomAD2 exomes

AF:

0.0121

AC:

2921

AN:

241526

AF XY:

0.0125

show subpopulations

Gnomad AFR exome

AF:

0.00506

Gnomad AMR exome

AF:

0.0106

Gnomad ASJ exome

AF:

0.00465

Gnomad EAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.0132

Gnomad NFE exome

AF:

0.0146

Gnomad OTH exome

AF:

0.0119

GnomAD4 exome

AF:

0.0144

AC:

20891

AN:

1451880

Hom.:

184

Cov.:

AF XY:

0.0144

AC XY:

10428

AN XY:

721828

show subpopulations

African (AFR)

AF:

0.00398

AC:

132

AN:

33182

American (AMR)

AF:

0.0107

AC:

464

AN:

43526

Ashkenazi Jewish (ASJ)

AF:

0.00514

AC:

133

AN:

25876

East Asian (EAS)

AF:

0.00159

AC:

AN:

39556

South Asian (SAS)

AF:

0.0168

AC:

1440

AN:

85820

European-Finnish (FIN)

AF:

0.0120

AC:

596

AN:

49854

Middle Eastern (MID)

AF:

0.00664

AC:

AN:

5722

European-Non Finnish (NFE)

AF:

0.0156

AC:

17243

AN:

1108324

Other (OTH)

AF:

0.0130

AC:

782

AN:

60020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1357

2713

4070

5426

6783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.0118

AC:

1805

AN:

152378

Hom.:

Cov.:

AF XY:

0.0125

AC XY:

931

AN XY:

74516

show subpopulations

African (AFR)

AF:

0.00459

AC:

191

AN:

41592

American (AMR)

AF:

0.0165

AC:

253

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.00518

AC:

AN:

3472

East Asian (EAS)

AF:

0.00251

AC:

AN:

5182

South Asian (SAS)

AF:

0.0184

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0120

AC:

127

AN:

10626

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0156

AC:

1061

AN:

68038

Other (OTH)

AF:

0.0180

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

186

279

372

465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0140

Hom.:

Bravo

AF:

0.0117

TwinsUK

AF:

0.0148

AC:

ALSPAC

AF:

0.0184

AC:

ESP6500AA

AF:

0.00568

AC:

ESP6500EA

AF:

0.0172

AC:

148

ExAC

AF:

0.0115

AC:

1392

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.0156

EpiControl

AF:

0.0148

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Candidiasis, familial, 9

Benign:1

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

0.17

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.085

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

Eigen

Benign

-0.29

Eigen_PC

Benign

-0.31

FATHMM_MKL

Benign

0.55

LIST_S2

Benign

0.78

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

MetaRNN

Benign

0.0070

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

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

.;.;.;L;.;.;.;.;.

PhyloP100

3.7

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-1.9

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

REVEL

Benign

0.091

Sift

Benign

0.10

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

Sift4G

Benign

0.12

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

Polyphen

0.70, 1.0, 0.51

.;P;.;D;P;.;P;.;.

Vest4

0.25

MPC

0.44

ClinPred

0.015

GERP RS

4.1

Varity_R

0.19

gMVP

0.62

Mutation Taster

=97/3

polymorphism

(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