rs4535195

chr3-57152007-A-Cchr3-57152007-A-T

Variant summary

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

The NM_017563.5(IL17RD):c.126+13154T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,914 control chromosomes in the GnomAD database, including 10,909 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 0.38 (10909 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

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]

LOC105377101 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5	c.126+13154T>G		intron_variant		ENST00000296318.12
LOC105377101	XR_940865.3	n.1836+213T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12	c.126+13154T>G		intron_variant		1	NM_017563.5	P1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57133 AN: 151794 Hom.: 10898 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.376 AC: 57169 AN: 151914 Hom.: 10909 Cov.: 32 AF XY: 0.381 AC XY: 28291 AN XY: 74234

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.382

Alfa AF: 0.376 Hom.: 6080

Bravo AF: 0.380

Asia WGS AF: 0.516 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.33

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: rs4535195; hg19: chr3-57186035;