rs12496746

chr3-57158899-A-G

Variant summary

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

The NM_017563.5(IL17RD):c.126+6262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,230 control chromosomes in the GnomAD database, including 1,455 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 0.11 (1455 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5	c.126+6262T>C		intron_variant		ENST00000296318.12
IL17RD	NM_001318864.2	c.-307+10333T>C		intron_variant
IL17RD	XM_005265238.5	c.42+6027T>C		intron_variant
IL17RD	XM_047448369.1	c.-444+6262T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12	c.126+6262T>C		intron_variant		1	NM_017563.5	P1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16736 AN: 152112 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.110 AC: 16766 AN: 152230 Hom.: 1455 Cov.: 32 AF XY: 0.118 AC XY: 8792 AN XY: 74426

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0975 Hom.: 998

Bravo AF: 0.115

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	5.6
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12496746; hg19: chr3-57192927;