NM_017563.5:c.2108-111delT

Variant names:

• chr3-57096615-TA-T
• rs56914717
• NM_017563.5:c.2108-111delT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017563.5(IL17RD):​c.2108-111delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 771,744 control chromosomes in the GnomAD database, including 15,306 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2693 hom., cov: 29)
  • Exomes 𝑓: 0.19 (12613 hom.)
• Consequence: IL17RD NM_017563.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.332
• Publications: 2 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)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 3-57096615-TA-T is Benign according to our data. Variant chr3-57096615-TA-T is described in ClinVar as Benign. ClinVar VariationId is 1220948.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RD	NM_017563.5	MANE Select	c.2108-111delT		intron	N/A	NP_060033.3	Q8NFM7-1
	IL17RD	NM_001318864.2		c.1676-111delT		intron	N/A	NP_001305793.1	Q8NFM7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RD	ENST00000296318.12	TSL:1 MANE Select	c.2108-111delT		intron	N/A	ENSP00000296318.7	Q8NFM7-1
	IL17RD	ENST00000320057.9	TSL:1	c.1676-111delT		intron	N/A	ENSP00000322250.5	Q8NFM7-2
	IL17RD	ENST00000463523.5	TSL:1	c.1676-111delT		intron	N/A	ENSP00000417516.1	Q8NFM7-2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26160 AN: 151966 Hom.: 2686 Cov.: 29

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.189 AC: 116887 AN: 619660 Hom.: 12613 AF XY: 0.189 AC XY: 62438 AN XY: 330972

African (AFR) AF: 0.114 AC: 1959 AN: 17200

American (AMR) AF: 0.362 AC: 13213 AN: 36546

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 3200 AN: 18424

East Asian (EAS) AF: 0.363 AC: 12764 AN: 35164

South Asian (SAS) AF: 0.210 AC: 13139 AN: 62444

European-Finnish (FIN) AF: 0.155 AC: 7465 AN: 48050

Middle Eastern (MID) AF: 0.174 AC: 620 AN: 3562

European-Non Finnish (NFE) AF: 0.160 AC: 58625 AN: 365964

Other (OTH) AF: 0.183 AC: 5902 AN: 32306

GnomAD4 genome AF: 0.172 AC: 26192 AN: 152084 Hom.: 2693 Cov.: 29 AF XY: 0.178 AC XY: 13210 AN XY: 74320

African (AFR) AF: 0.117 AC: 4866 AN: 41514

American (AMR) AF: 0.291 AC: 4449 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1850 AN: 5146

South Asian (SAS) AF: 0.234 AC: 1124 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1753 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10889 AN: 67978

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.165 Hom.: 276

Bravo AF: 0.179

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.33
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: rs56914717; hg19: chr3-57130643;