chr3-57134313-C-T

Variant names:

• chr3-57134313-C-T
• rs6788981
• NM_017563.5:c.127-14000G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017563.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RD	NM_017563.5	MANE Select	c.127-14000G>A		intron	N/A	NP_060033.3	Q8NFM7-1
	IL17RD	NM_001318864.2		c.-306-14000G>A		intron	N/A	NP_001305793.1	Q8NFM7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RD	ENST00000296318.12	TSL:1 MANE Select	c.127-14000G>A		intron	N/A	ENSP00000296318.7	Q8NFM7-1
	IL17RD	ENST00000320057.9	TSL:1	c.-306-14000G>A		intron	N/A	ENSP00000322250.5	Q8NFM7-2
	IL17RD	ENST00000463523.5	TSL:1	c.-307+8140G>A		intron	N/A	ENSP00000417516.1	Q8NFM7-2

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

African (AFR) AF: 0.433 AC: 6655 AN: 15368

American (AMR) AF: 0.388 AC: 15207 AN: 39190

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 2834 AN: 16944

East Asian (EAS) AF: 0.390 AC: 11983 AN: 30702

South Asian (SAS) AF: 0.207 AC: 13469 AN: 65112

European-Finnish (FIN) AF: 0.190 AC: 7365 AN: 38760

Middle Eastern (MID) AF: 0.237 AC: 655 AN: 2766

European-Non Finnish (NFE) AF: 0.151 AC: 44545 AN: 295078

Other (OTH) AF: 0.206 AC: 5654 AN: 27474

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

African (AFR) AF: 0.419 AC: 17365 AN: 41470

American (AMR) AF: 0.314 AC: 4801 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1944 AN: 5166

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2076 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9456 AN: 67978

Other (OTH) AF: 0.242 AC: 512 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	5.6
DANN	Benign	0.82
PhyloP100		2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6788981; hg19: chr3-57168341; COSMIC: COSV56341020;