chr3-57102557-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017563.5(IL17RD):c.901G>A(p.Val301Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,574,568 control chromosomes in the GnomAD database, including 25,963 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2470 hom., cov: 33)

Exomes 𝑓: 0.17 ( 23493 hom. )

Consequence

IL17RD
NM_017563.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.49

Publications

22 publications found

Variant links:

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]

IL17RD Gene-Disease associations (from GenCC):

Kallmann syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
hypogonadotropic hypogonadism 18 with or without anosmia
Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

IL17RD links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0021972358).

BP6

Variant 3-57102557-C-T is Benign according to our data. Variant chr3-57102557-C-T is described in ClinVar as Benign. ClinVar VariationId is 1262347.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RD	NM_017563.5	MANE Select	c.901G>A	p.Val301Met	missense	Exon 10 of 13	NP_060033.3
	IL17RD	NM_001318864.2		c.469G>A	p.Val157Met	missense	Exon 11 of 14	NP_001305793.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
IL17RD	ENST00000296318.12	TSL:1 MANE Select	c.901G>A	p.Val301Met	missense	Exon 10 of 13	ENSP00000296318.7
IL17RD	ENST00000320057.9	TSL:1	c.469G>A	p.Val157Met	missense	Exon 11 of 14	ENSP00000322250.5
IL17RD	ENST00000463523.5	TSL:1	c.469G>A	p.Val157Met	missense	Exon 10 of 13	ENSP00000417516.1

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24098

AN:

151008

Hom.:

2463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0691

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.178

GnomAD2 exomes

AF:

0.204

AC:

50695

AN:

248048

AF XY:

0.200

show subpopulations

Gnomad AFR exome

AF:

0.0638

Gnomad AMR exome

AF:

0.367

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.370

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.172

AC:

244330

AN:

1423434

Hom.:

23493

Cov.:

AF XY:

0.173

AC XY:

121487

AN XY:

704168

show subpopulations

African (AFR)

AF:

0.0609

AC:

2002

AN:

32856

American (AMR)

AF:

0.356

AC:

15632

AN:

43860

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

4356

AN:

25478

East Asian (EAS)

AF:

0.365

AC:

14131

AN:

38742

South Asian (SAS)

AF:

0.205

AC:

16981

AN:

82942

European-Finnish (FIN)

AF:

0.155

AC:

8182

AN:

52736

Middle Eastern (MID)

AF:

0.175

AC:

979

AN:

5610

European-Non Finnish (NFE)

AF:

0.159

AC:

171849

AN:

1082714

Other (OTH)

AF:

0.175

AC:

10218

AN:

58496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

8326

16651

24977

33302

41628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6432

12864

19296

25728

32160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.160

AC:

24124

AN:

151134

Hom.:

2470

Cov.:

AF XY:

0.165

AC XY:

12228

AN XY:

73900

show subpopulations

African (AFR)

AF:

0.0693

AC:

2852

AN:

41172

American (AMR)

AF:

0.288

AC:

4382

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

612

AN:

3450

East Asian (EAS)

AF:

0.367

AC:

1877

AN:

5114

South Asian (SAS)

AF:

0.238

AC:

1133

AN:

4758

European-Finnish (FIN)

AF:

0.166

AC:

1744

AN:

10484

Middle Eastern (MID)

AF:

0.168

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.161

AC:

10893

AN:

67648

Other (OTH)

AF:

0.178

AC:

373

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

999

1997

2996

3994

4993

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.166

Hom.:

7463

Bravo

AF:

0.163

TwinsUK

AF:

0.147

AC:

545

ALSPAC

AF:

0.155

AC:

597

ESP6500AA

AF:

0.0719

AC:

317

ESP6500EA

AF:

0.152

AC:

1306

ExAC

AF:

0.196

AC:

23760

Asia WGS

AF:

0.305

AC:

1056

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.88

DEOGEN2

Benign

0.051

Eigen

Benign

-0.51

Eigen_PC

Benign

-0.44

FATHMM_MKL

Benign

0.61

LIST_S2

Benign

0.82

MetaRNN

Benign

0.0022

MetaSVM

Benign

-0.93

MutationAssessor

Benign

0.34

PhyloP100

1.5

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.30

REVEL

Benign

0.085

Sift

Benign

0.35

Sift4G

Benign

0.39

Polyphen

0.47

Vest4

0.16

MPC

0.30

ClinPred

0.014

GERP RS

3.6

Varity_R

0.030

gMVP

0.27

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over