rs279545

chr3-9930809-G-Achr3-9930809-G-C

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.1339-86G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,198,708 control chromosomes in the GnomAD database, including 351,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.65 (35824 hom., cov: 33)
  • Exomes 𝑓: 0.77 (315842 hom.)
• Consequence: IL17RC NM_153460.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.226

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=-0.87).
• BP6: Variant 3-9930809-G-A is Benign according to our data. Variant chr3-9930809-G-A is described in ClinVar as [Benign]. Clinvar id is 2687937.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RC	NM_153460.4	c.1339-86G>A		intron_variant		ENST00000403601.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RC	ENST00000403601.8	c.1339-86G>A		intron_variant		1	NM_153460.4	P4

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98316 AN: 152024 Hom.: 35813 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.691

GnomAD4 exome AF: 0.771 AC: 807290 AN: 1046568 Hom.: 315842 Cov.: 15 AF XY: 0.772 AC XY: 416634 AN XY: 539714

Gnomad4 AFR exome AF: 0.266

Gnomad4 AMR exome AF: 0.702

Gnomad4 ASJ exome AF: 0.815

Gnomad4 EAS exome AF: 0.795

Gnomad4 SAS exome AF: 0.737

Gnomad4 FIN exome AF: 0.843

Gnomad4 NFE exome AF: 0.790

Gnomad4 OTH exome AF: 0.756

GnomAD4 genome AF: 0.647 AC: 98364 AN: 152140 Hom.: 35824 Cov.: 33 AF XY: 0.655 AC XY: 48700 AN XY: 74380

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.693

Alfa AF: 0.746 Hom.: 25121

Bravo AF: 0.618

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 94% of patients studied by a panel of primary immunodeficiencies. Number of patients: 89. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.5
Dann	Benign	0.72

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: rs279545; hg19: chr3-9972493; COSMIC: COSV55972637; COSMIC: COSV55972637;