chr3-53855822-T-C

Variant names:

• chr3-53855822-T-C
• rs999514
• NM_018725.4:c.529+481T>C

Variant summary

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

The NM_018725.4(IL17RB):​c.529+481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,076 control chromosomes in the GnomAD database, including 20,462 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 0.50 (20462 hom., cov: 32)
• Consequence: IL17RB NM_018725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 14 publications found

Genes affected

IL17RB (HGNC:18015): (interleukin 17 receptor B) The protein encoded by this gene is a cytokine receptor. This receptor specifically binds to IL17B and IL17E, but does not bind to IL17 and IL17C. This receptor has been shown to mediate the activation of NF-kappaB and the production of IL8 induced by IL17E. The expression of the rat counterpart of this gene was found to be significantly up-regulated during intestinal inflammation, which suggested the immunoregulatory activity of this receptor. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018725.4. 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
	IL17RB	NM_018725.4	MANE Select	c.529+481T>C		intron	N/A	NP_061195.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RB	ENST00000288167.8	TSL:1 MANE Select	c.529+481T>C		intron	N/A	ENSP00000288167.3	Q9NRM6-1
	IL17RB	ENST00000899729.1		c.703+481T>C		intron	N/A	ENSP00000569788.1
	IL17RB	ENST00000899731.1		c.703+481T>C		intron	N/A	ENSP00000569790.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75852 AN: 151958 Hom.: 20426 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.499 AC: 75938 AN: 152076 Hom.: 20462 Cov.: 32 AF XY: 0.506 AC XY: 37587 AN XY: 74350

African (AFR) AF: 0.617 AC: 25583 AN: 41478

American (AMR) AF: 0.571 AC: 8729 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3470

East Asian (EAS) AF: 0.948 AC: 4912 AN: 5180

South Asian (SAS) AF: 0.599 AC: 2886 AN: 4820

European-Finnish (FIN) AF: 0.391 AC: 4134 AN: 10576

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26759 AN: 67964

Other (OTH) AF: 0.468 AC: 985 AN: 2106

Alfa AF: 0.440 Hom.: 46539

Bravo AF: 0.518

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.27
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs999514; hg19: chr3-53889849;