rs2082697263

Variant names:

• chr3-9904082-A-C
• rs2082697263
• NM_153480.2:c.199A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-9904082-A-C
• chr3-9904082-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_153480.2(IL17RE):​c.199A>C​(p.Lys67Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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)
• Consequence: IL17RE NM_153480.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12698224).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RE	NM_153480.2	c.199A>C	p.Lys67Gln	missense_variant	Exon 3 of 16	ENST00000383814.8	NP_705613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RE	ENST00000383814.8	c.199A>C	p.Lys67Gln	missense_variant	Exon 3 of 16	1	NM_153480.2	ENSP00000373325.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.9
DANN	Benign	0.88
DEOGEN2	Benign	0.0047	.;T;.
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.095	N
LIST_S2	Benign	0.51	T;T;T
M_CAP	Benign	0.0043	T
MetaRNN	Benign	0.13	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	.;L;L
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-0.29	N;N;N
REVEL	Benign	0.021
Sift	Uncertain	0.016	D;D;D
Sift4G	Benign	0.14	T;T;T
Polyphen		0.12, 0.19	.;B;B
Vest4		0.26
MutPred		0.43		.;Loss of ubiquitination at K67 (P = 0.0224);Loss of ubiquitination at K67 (P = 0.0224);
MVP		0.24
ClinPred		0.093	T
GERP RS		1.6
Varity_R		0.30
gMVP		0.15

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: rs2082697263; hg19: chr3-9945766;