3-57123688-G-A

Position:

• chr3-57123688-G-A

Variant summary

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

The NM_017563.5(IL17RD):​c.127-3375C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,138 control chromosomes in the GnomAD database, including 3,719 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 0.20 (3719 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RD	NM_017563.5	c.127-3375C>T		intron_variant		ENST00000296318.12	NP_060033.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RD	ENST00000296318.12	c.127-3375C>T		intron_variant		1	NM_017563.5	ENSP00000296318	P1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31183 AN: 152020 Hom.: 3715 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.205 AC: 31188 AN: 152138 Hom.: 3719 Cov.: 32 AF XY: 0.201 AC XY: 14933 AN XY: 74384

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.202

Alfa AF: 0.261 Hom.: 7031

Bravo AF: 0.200

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74

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: rs6810042; hg19: chr3-57157716;