3-57096615-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017563.5(IL17RD):c.2108-111del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 771,744 control chromosomes in the GnomAD database, including 15,306 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2693 hom., cov: 29)
  • Exomes 𝑓: 0.19 (12613 hom.)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.332

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 -10 ACMG points.

• BP6: Variant 3-57096615-TA-T is Benign according to our data. Variant chr3-57096615-TA-T is described in ClinVar as [Benign]. Clinvar id is 1220948.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5	c.2108-111del		intron_variant		ENST00000296318.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12	c.2108-111del		intron_variant		1	NM_017563.5	P1
IL17RD	ENST00000320057.9	c.1676-111del		intron_variant		1
IL17RD	ENST00000463523.5	c.1676-111del		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26160 AN: 151966 Hom.: 2686 Cov.: 29

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.189 AC: 116887 AN: 619660 Hom.: 12613 AF XY: 0.189 AC XY: 62438 AN XY: 330972

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.362

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.363

Gnomad4 SAS exome AF: 0.210

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.172 AC: 26192 AN: 152084 Hom.: 2693 Cov.: 29 AF XY: 0.178 AC XY: 13210 AN XY: 74320

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.186

Alfa AF: 0.165 Hom.: 276

Bravo AF: 0.179

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs56914717; hg19: chr3-57130643;