rs4535195

Variant names:

• chr3-57152007-A-C
• rs4535195
• NM_017563.5:c.126+13154T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-57152007-A-C
• chr3-57152007-A-T

Variant summary

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

The NM_017563.5(IL17RD):​c.126+13154T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,914 control chromosomes in the GnomAD database, including 10,909 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 0.38 (10909 hom., cov: 32)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 4 publications found

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)

LOC105377101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RD	NM_017563.5	c.126+13154T>G		intron_variant	Intron 1 of 12	ENST00000296318.12	NP_060033.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RD	ENST00000296318.12	c.126+13154T>G		intron_variant	Intron 1 of 12	1	NM_017563.5	ENSP00000296318.7

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57133 AN: 151794 Hom.: 10898 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.380

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.376 AC: 57169 AN: 151914 Hom.: 10909 Cov.: 32 AF XY: 0.381 AC XY: 28291 AN XY: 74234

African (AFR) AF: 0.324 AC: 13411 AN: 41412

American (AMR) AF: 0.459 AC: 6998 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1107 AN: 3462

East Asian (EAS) AF: 0.542 AC: 2797 AN: 5164

South Asian (SAS) AF: 0.472 AC: 2270 AN: 4814

European-Finnish (FIN) AF: 0.382 AC: 4029 AN: 10552

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25319 AN: 67944

Other (OTH) AF: 0.382 AC: 804 AN: 2106

Alfa AF: 0.371 Hom.: 8693

Bravo AF: 0.380

Asia WGS AF: 0.516 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.44
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: rs4535195; hg19: chr3-57186035;