19-18080631-A-C

Position:

• chr19-18080631-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005535.3(IL12RB1):​c.409+201T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,196 control chromosomes in the GnomAD database, including 1,995 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 0.14 (1995 hom., cov: 31)
• Consequence: IL12RB1 NM_005535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

Genes affected

IL12RB1 (HGNC:5971): (interleukin 12 receptor subunit beta 1) The protein encoded by this gene is a type I transmembrane protein that belongs to the hemopoietin receptor superfamily. This protein binds to interleukine 12 (IL12) with a low affinity, and is thought to be a part of IL12 receptor complex. This protein forms a disulfide-linked oligomer, which is required for its IL12 binding activity. The coexpression of this and IL12RB2 proteins was shown to lead to the formation of high-affinity IL12 binding sites and reconstitution of IL12 dependent signaling. Mutations in this gene impair the development of interleukin-17-producing T lymphocytes and result in increased susceptibility to mycobacterial and Salmonella infections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12RB1	NM_005535.3	c.409+201T>G		intron_variant		ENST00000593993.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12RB1	ENST00000593993.7	c.409+201T>G		intron_variant		1	NM_005535.3	P1
IL12RB1	ENST00000322153.11	c.409+201T>G		intron_variant		1
IL12RB1	ENST00000600835.6	c.409+201T>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21740 AN: 152078 Hom.: 1992 Cov.: 31

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.143 AC: 21749 AN: 152196 Hom.: 1995 Cov.: 31 AF XY: 0.143 AC XY: 10650 AN XY: 74398

Gnomad4 AFR AF: 0.0357

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.146

Alfa AF: 0.113 Hom.: 274

Bravo AF: 0.128

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs2305742; hg19: chr19-18191441;