3-57119841-C-T

Position:

• chr3-57119841-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017563.5(IL17RD):​c.184+415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,200 control chromosomes in the GnomAD database, including 2,475 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2475 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

IL17RD (HGNC:17616): (interleukin 17 receptor D) This gene encodes a membrane protein belonging to the interleukin-17 receptor (IL-17R) protein family. The encoded protein is a component of the interleukin-17 receptor signaling complex, and the interaction between this protein and IL-17R does not require the interleukin. The gene product also affects fibroblast growth factor signaling, inhibiting or stimulating growth through MAPK/ERK signaling. Alternate splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5	c.184+415G>A		intron_variant		ENST00000296318.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12	c.184+415G>A		intron_variant		1	NM_017563.5	P1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24123 AN: 152082 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.175

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.159 AC: 24145 AN: 152200 Hom.: 2475 Cov.: 32 AF XY: 0.164 AC XY: 12235 AN XY: 74402

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.175

Alfa AF: 0.170 Hom.: 1241

Bravo AF: 0.163

Asia WGS AF: 0.304 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.44

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: rs747089; hg19: chr3-57153869;