rs115949142

chr3-9924029-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_153460.4(IL17RC):c.762+9T>A variant causes a intron 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 NM_153460.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.823

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 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 id is 475931.Status of the report is criteria_provided_single_submitter, 1 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/exons	MANE	UniProt
IL17RC	NM_153460.4	c.762+9T>A		intron_variant		ENST00000403601.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RC	ENST00000403601.8	c.762+9T>A		intron_variant		1	NM_153460.4	P4

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4122 AN: 152036 Hom.: 79 Cov.: 31

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

GnomAD3 exomes AF: 0.0315 AC: 7875 AN: 250242 Hom.: 178 AF XY: 0.0345 AC XY: 4671 AN XY: 135382

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 SAS exome AF: 0.0656

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.: 32 AF XY: 0.0377 AC XY: 27399 AN XY: 726726

Gnomad4 AFR exome AF: 0.00475

Gnomad4 AMR exome AF: 0.0150

Gnomad4 ASJ exome AF: 0.0491

Gnomad4 EAS exome AF: 0.000403

Gnomad4 SAS exome AF: 0.0668

Gnomad4 FIN exome AF: 0.0297

Gnomad4 NFE exome AF: 0.0375

Gnomad4 OTH exome AF: 0.0339

GnomAD4 genome AF: 0.0271 AC: 4124 AN: 152154 Hom.: 80 Cov.: 31 AF XY: 0.0276 AC XY: 2055 AN XY: 74382

Gnomad4 AFR AF: 0.00648

Gnomad4 AMR AF: 0.0224

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0380

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0349 Hom.: 31

Bravo AF: 0.0239

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Candidiasis, familial, 9 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	4.4
Dann	Benign	0.86
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

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

Other links and lift over

dbSNP: rs115949142; hg19: chr3-9965713;