chr3-57149849-T-C

Position:

• chr3-57149849-T-C

Variant summary

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

The NM_017563.5(IL17RD):​c.126+15312A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,106 control chromosomes in the GnomAD database, including 7,161 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 0.28 (7161 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RD	NM_017563.5	c.126+15312A>G		intron_variant		ENST00000296318.12	NP_060033.3
LOC105377101	XR_940865.3	n.2484A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RD	ENST00000296318.12	c.126+15312A>G		intron_variant		1	NM_017563.5	ENSP00000296318	P1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42610 AN: 151988 Hom.: 7133 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.281 AC: 42700 AN: 152106 Hom.: 7161 Cov.: 32 AF XY: 0.288 AC XY: 21438 AN XY: 74368

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.277

Alfa AF: 0.215 Hom.: 1984

Bravo AF: 0.299

Asia WGS AF: 0.427 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.82

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: rs17216900; hg19: chr3-57183877;