3-53865249-C-T

Variant names:

• chr3-53865249-C-T
• rs1043261
• NM_018725.4:c.1450C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018725.4(IL17RB):​c.1450C>T​(p.Gln484*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 1,611,796 control chromosomes in the GnomAD database, including 7,228 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 0.088 (710 hom., cov: 32)
  • Exomes 𝑓: 0.088 (6518 hom.)
• Consequence: IL17RB NM_018725.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 44 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]

ACTR8 (HGNC:14672): (actin related protein 8) Predicted to enable ATP binding activity. Predicted to be involved in chromatin remodeling; double-strand break repair; and regulation of transcription, DNA-templated. Located in centrosome and nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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.1450C>T	p.Gln484*	stop_gained	Exon 11 of 11	NP_061195.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RB	ENST00000288167.8	TSL:1 MANE Select	c.1450C>T	p.Gln484*	stop_gained	Exon 11 of 11	ENSP00000288167.3	Q9NRM6-1
	IL17RB	ENST00000899729.1		c.1711C>T	p.Gln571*	stop_gained	Exon 13 of 13	ENSP00000569788.1
	IL17RB	ENST00000899731.1		c.1624C>T	p.Gln542*	stop_gained	Exon 12 of 12	ENSP00000569790.1

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13383 AN: 152088 Hom.: 707 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0948

GnomAD2 exomes AF: 0.0996 AC: 24849 AN: 249524 AF XY: 0.103

Gnomad AFR exome AF: 0.0885

Gnomad AMR exome AF: 0.0935

Gnomad ASJ exome AF: 0.0731

Gnomad EAS exome AF: 0.195

Gnomad FIN exome AF: 0.0399

Gnomad NFE exome AF: 0.0791

Gnomad OTH exome AF: 0.0914

GnomAD4 exome AF: 0.0879 AC: 128310 AN: 1459590 Hom.: 6518 Cov.: 33 AF XY: 0.0908 AC XY: 65923 AN XY: 726202

African (AFR) AF: 0.0859 AC: 2876 AN: 33472

American (AMR) AF: 0.0930 AC: 4161 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 1793 AN: 26134

East Asian (EAS) AF: 0.144 AC: 5735 AN: 39698

South Asian (SAS) AF: 0.178 AC: 15338 AN: 86248

European-Finnish (FIN) AF: 0.0384 AC: 1974 AN: 51344

Middle Eastern (MID) AF: 0.0928 AC: 533 AN: 5742

European-Non Finnish (NFE) AF: 0.0809 AC: 89974 AN: 1111868

Other (OTH) AF: 0.0982 AC: 5926 AN: 60366

GnomAD4 genome AF: 0.0881 AC: 13413 AN: 152206 Hom.: 710 Cov.: 32 AF XY: 0.0890 AC XY: 6623 AN XY: 74402

African (AFR) AF: 0.0886 AC: 3677 AN: 41520

American (AMR) AF: 0.101 AC: 1543 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1015 AN: 5178

South Asian (SAS) AF: 0.185 AC: 893 AN: 4818

European-Finnish (FIN) AF: 0.0433 AC: 459 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0787 AC: 5352 AN: 68012

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

Alfa AF: 0.0851 Hom.: 2954

Bravo AF: 0.0886

TwinsUK AF: 0.0833 AC: 309

ALSPAC AF: 0.0760 AC: 293

ESP6500AA AF: 0.0937 AC: 413

ESP6500EA AF: 0.0790 AC: 679

ExAC AF: 0.0986 AC: 11976

Asia WGS AF: 0.205 AC: 711 AN: 3478

EpiCase AF: 0.0796

EpiControl AF: 0.0797

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.055	T
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	36
DANN	Uncertain	0.98
Eigen	Uncertain	0.32
Eigen_PC	Benign	0.026
FATHMM_MKL	Benign	0.20	N
PhyloP100		0.25
Vest4		0.57
GERP RS		2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=158/42	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: rs1043261; hg19: chr3-53899276; COSMIC: COSV107225600; COSMIC: COSV107225600;