3-57134313-C-T

Position:

• chr3-57134313-C-T

Variant summary

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

The NM_017563.5(IL17RD):​c.127-14000G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 683,486 control chromosomes in the GnomAD database, including 19,330 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 0.25 (6030 hom., cov: 33)
  • Exomes 𝑓: 0.20 (13300 hom.)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

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]

RPL19P2 (HGNC:29946): (ribosomal protein L19 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5	c.127-14000G>A		intron_variant		ENST00000296318.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12	c.127-14000G>A		intron_variant		1	NM_017563.5	P1
RPL19P2	ENST00000438827.1	n.172C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38030 AN: 151974 Hom.: 6002 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.204 AC: 108367 AN: 531394 Hom.: 13300 Cov.: 4 AF XY: 0.199 AC XY: 58128 AN XY: 292010

Gnomad4 AFR exome AF: 0.433

Gnomad4 AMR exome AF: 0.388

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.390

Gnomad4 SAS exome AF: 0.207

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.251 AC: 38111 AN: 152092 Hom.: 6030 Cov.: 33 AF XY: 0.257 AC XY: 19118 AN XY: 74360

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.242

Alfa AF: 0.220 Hom.: 783

Bravo AF: 0.266

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	5.6
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: rs6788981; hg19: chr3-57168341; COSMIC: COSV56341020;