3-9906313-C-T

Variant names:

• chr3-9906313-C-T
• rs279581
• NM_153480.2:c.269-51C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153480.2(IL17RE):​c.269-51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,002,022 control chromosomes in the GnomAD database, including 139,617 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 0.56 (24363 hom., cov: 32)
  • Exomes 𝑓: 0.51 (115254 hom.)
• Consequence: IL17RE NM_153480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 14 publications found

Genes affected

IL17RE (HGNC:18439): (interleukin 17 receptor E) This gene encodes a transmembrane protein that functions as the receptor for interleukin-17C. The encoded protein signals to downstream components of the mitogen activated protein kinase (MAPK) pathway. Activity of this protein is important in the immune response to bacterial pathogens. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153480.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RE	NM_153480.2	MANE Select	c.269-51C>T		intron	N/A	NP_705613.1
	IL17RE	NM_153483.2		c.389-51C>T		intron	N/A	NP_705616.2
	IL17RE	NM_153481.2		c.-80-51C>T		intron	N/A	NP_705614.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RE	ENST00000383814.8	TSL:1 MANE Select	c.269-51C>T		intron	N/A	ENSP00000373325.3
	IL17RE	ENST00000421412.5	TSL:1	c.368-51C>T		intron	N/A	ENSP00000404916.1
	IL17RE	ENST00000454190.6	TSL:2	c.269-51C>T		intron	N/A	ENSP00000388086.2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84354 AN: 151872 Hom.: 24316 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.550

GnomAD2 exomes AF: 0.490 AC: 112813 AN: 230278 AF XY: 0.489

Gnomad AFR exome AF: 0.668

Gnomad AMR exome AF: 0.457

Gnomad ASJ exome AF: 0.467

Gnomad EAS exome AF: 0.0808

Gnomad FIN exome AF: 0.587

Gnomad NFE exome AF: 0.545

Gnomad OTH exome AF: 0.514

GnomAD4 exome AF: 0.508 AC: 431909 AN: 850032 Hom.: 115254 Cov.: 11 AF XY: 0.506 AC XY: 224339 AN XY: 443442

African (AFR) AF: 0.661 AC: 13977 AN: 21154

American (AMR) AF: 0.464 AC: 18812 AN: 40582

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 9897 AN: 21324

East Asian (EAS) AF: 0.0815 AC: 2984 AN: 36596

South Asian (SAS) AF: 0.418 AC: 27927 AN: 66842

European-Finnish (FIN) AF: 0.579 AC: 29488 AN: 50960

Middle Eastern (MID) AF: 0.576 AC: 2467 AN: 4286

European-Non Finnish (NFE) AF: 0.538 AC: 305848 AN: 568462

Other (OTH) AF: 0.515 AC: 20509 AN: 39826

GnomAD4 genome AF: 0.556 AC: 84458 AN: 151990 Hom.: 24363 Cov.: 32 AF XY: 0.552 AC XY: 41000 AN XY: 74298

African (AFR) AF: 0.661 AC: 27392 AN: 41440

American (AMR) AF: 0.524 AC: 8010 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3470

East Asian (EAS) AF: 0.0833 AC: 431 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4822

European-Finnish (FIN) AF: 0.586 AC: 6185 AN: 10560

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36979 AN: 67938

Other (OTH) AF: 0.556 AC: 1173 AN: 2108

Alfa AF: 0.536 Hom.: 12286

Bravo AF: 0.555

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.68
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs279581; hg19: chr3-9947997;