ENST00000469686.6:n.1132T>A

Variant names:

Variant summary

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

The ENST00000469686.6(IL17RC):n.1132T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 1,612,906 control chromosomes in the GnomAD database, including 1,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 80 hom., cov: 31)

Exomes 𝑓: 0.037 ( 1151 hom. )

Consequence

IL17RC
ENST00000469686.6 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.823

Publications

4 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 (BayesDel_noAF=-0.7).

BP6

Variant 3-9924029-T-A is Benign according to our data. Variant chr3-9924029-T-A is described in ClinVar as Benign. ClinVar VariationId is 475931.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RC	NM_153460.4 link	c.762+9T>A		intron_variant	Intron 8 of 18	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.762+9T>A		intron_variant	Intron 8 of 18	1	NM_153460.4	ENSP00000384969.3		Q8NAC3-2
ENSG00000288550	ENST00000683484.1 link	n.678+48T>A		intron_variant	Intron 7 of 23			ENSP00000507040.1		A0A804HIF2

Frequencies

GnomAD3 genomes

AF:

0.0271

AC:

4122

AN:

152036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00650

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0225

Gnomad ASJ

AF:

0.0441

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0612

Gnomad FIN

AF:

0.0307

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0380

Gnomad OTH

AF:

0.0273

GnomAD2 exomes

AF:

0.0315

AC:

7875

AN:

250242

AF XY:

0.0345

show subpopulations

Gnomad AFR exome

AF:

0.00617

Gnomad AMR exome

AF:

0.0140

Gnomad ASJ exome

AF:

0.0508

Gnomad EAS exome

AF:

0.000544

Gnomad FIN exome

AF:

0.0292

Gnomad NFE exome

AF:

0.0349

Gnomad OTH exome

AF:

0.0313

GnomAD4 exome

AF:

0.0366

AC:

53406

AN:

1460752

Hom.:

1151

Cov.:

AF XY:

0.0377

AC XY:

27399

AN XY:

726726

show subpopulations

African (AFR)

AF:

0.00475

AC:

159

AN:

33480

American (AMR)

AF:

0.0150

AC:

670

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0491

AC:

1284

AN:

26132

East Asian (EAS)

AF:

0.000403

AC:

AN:

39700

South Asian (SAS)

AF:

0.0668

AC:

5760

AN:

86254

European-Finnish (FIN)

AF:

0.0297

AC:

1554

AN:

52334

Middle Eastern (MID)

AF:

0.0425

AC:

245

AN:

5766

European-Non Finnish (NFE)

AF:

0.0375

AC:

41670

AN:

1111976

Other (OTH)

AF:

0.0339

AC:

2048

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

3013

6026

9040

12053

15066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1594

3188

4782

6376

7970

<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:

0.0271

AC:

4124

AN:

152154

Hom.:

Cov.:

AF XY:

0.0276

AC XY:

2055

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.00648

AC:

269

AN:

41508

American (AMR)

AF:

0.0224

AC:

343

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0441

AC:

153

AN:

3468

East Asian (EAS)

AF:

0.00213

AC:

AN:

5166

South Asian (SAS)

AF:

0.0619

AC:

298

AN:

4816

European-Finnish (FIN)

AF:

0.0307

AC:

325

AN:

10600

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0380

AC:

2584

AN:

67988

Other (OTH)

AF:

0.0270

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

204

407

611

814

1018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0349

Hom.:

Bravo

AF:

0.0239

Asia WGS

AF:

0.0200

AC:

AN:

3478

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 03, 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

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.4

(source)

DANN

Benign

0.86

PhyloP100

-0.82

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Mutation Taster

=100/0

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