rs279581

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-9906313-C-A
• chr3-9906313-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153480.2(IL17RE):​c.269-51C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000469 in 852,286 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000047 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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>A		intron	N/A	NP_705613.1
	IL17RE	NM_153483.2		c.389-51C>A		intron	N/A	NP_705616.2
	IL17RE	NM_153481.2		c.-80-51C>A		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>A		intron	N/A	ENSP00000373325.3
	IL17RE	ENST00000421412.5	TSL:1	c.368-51C>A		intron	N/A	ENSP00000404916.1
	IL17RE	ENST00000454190.6	TSL:2	c.269-51C>A		intron	N/A	ENSP00000388086.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000434 AC: 1 AN: 230278 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000489

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000469 AC: 4 AN: 852286 Hom.: 0 Cov.: 11 AF XY: 0.00000450 AC XY: 2 AN XY: 444596

African (AFR) AF: 0.00 AC: 0 AN: 21196

American (AMR) AF: 0.00 AC: 0 AN: 40650

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21374

East Asian (EAS) AF: 0.00 AC: 0 AN: 36612

South Asian (SAS) AF: 0.00 AC: 0 AN: 67056

European-Finnish (FIN) AF: 0.0000784 AC: 4 AN: 51026

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4298

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 570160

Other (OTH) AF: 0.00 AC: 0 AN: 39914

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.63
PhyloP100		-1.5

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;