rs6445854

Variant names:

• chr3-57108066-T-C
• rs6445854
• NM_017563.5:c.550+1471A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-57108066-T-C
• chr3-57108066-T-G

Variant summary

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

The NM_017563.5(IL17RD):​c.550+1471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,846 control chromosomes in the GnomAD database, including 3,842 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 0.22 (3842 hom., cov: 31)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• 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)

ENSG00000297895 (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 (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RD	NM_017563.5	c.550+1471A>G		intron_variant	Intron 5 of 12	ENST00000296318.12	NP_060033.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RD	ENST00000296318.12	c.550+1471A>G		intron_variant	Intron 5 of 12	1	NM_017563.5	ENSP00000296318.7

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32861 AN: 151730 Hom.: 3835 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.217 AC: 32890 AN: 151846 Hom.: 3842 Cov.: 31 AF XY: 0.218 AC XY: 16173 AN XY: 74194

African (AFR) AF: 0.265 AC: 10977 AN: 41380

American (AMR) AF: 0.155 AC: 2362 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.0715 AC: 371 AN: 5190

South Asian (SAS) AF: 0.231 AC: 1108 AN: 4804

European-Finnish (FIN) AF: 0.275 AC: 2884 AN: 10486

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13470 AN: 67934

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.203 Hom.: 3574

Bravo AF: 0.208

Asia WGS AF: 0.155 AC: 542 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	5.3
DANN	Benign	0.72
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6445854; hg19: chr3-57142094;