Genetic Variant NM_153480.2:c.269-51C>T (chr3-9906313-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

14 publications found

Variant links:

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]

IL17RE links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RE	NM_153480.2 link	c.269-51C>T		intron_variant	Intron 3 of 15	ENST00000383814.8	NP_705613.1	Q8NFR9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RE	ENST00000383814.8 link	c.269-51C>T		intron_variant	Intron 3 of 15	1	NM_153480.2	ENSP00000373325.3		Q8NFR9-1

Frequencies

GnomAD3 genomes

AF:

0.555

AC:

84354

AN:

151872

Hom.:

24316

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.506

AC XY:

224339

AN XY:

443442

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

9686

19372

29059

38745

48431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.556

AC:

84458

AN:

151990

Hom.:

24363

Cov.:

AF XY:

0.552

AC XY:

41000

AN XY:

74298

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1853

3706

5559

7412

9265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.41

(source)

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)

(source)

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

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NM_153480.2:c.269-51C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over