chr19-18072285-C-T

Position:

chr19-18072285-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_005535.3(IL12RB1):c.848G>A(p.Arg283Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00862 in 1,613,976 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0060 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0089 ( 79 hom. )

Consequence

IL12RB1
NM_005535.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.76

Variant links:

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]

IL12RB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007248014).

BP6

Variant 19-18072285-C-T is Benign according to our data. Variant chr19-18072285-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 474979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-18072285-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.006 (913/152230) while in subpopulation NFE AF= 0.00929 (632/68016). AF 95% confidence interval is 0.00869. There are 0 homozygotes in gnomad4. There are 443 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12RB1	NM_005535.3 linkuse as main transcript	c.848G>A	p.Arg283Gln	missense_variant	9/17	ENST00000593993.7	NP_005526.1	P42701-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL12RB1	ENST00000593993.7 linkuse as main transcript	c.848G>A	p.Arg283Gln	missense_variant	9/17	1	NM_005535.3	ENSP00000472165.2	P42701-1
IL12RB1	ENST00000600835.6 linkuse as main transcript	c.848G>A	p.Arg283Gln	missense_variant	10/18	1		ENSP00000470788.1	P42701-1
IL12RB1	ENST00000322153.11 linkuse as main transcript	c.848G>A	p.Arg283Gln	missense_variant	9/10	1		ENSP00000314425.5	P42701-3

Frequencies

GnomAD3 genomes

AF:

0.00600

AC:

912

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00159

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00374

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00929

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00611

AC:

1534

AN:

251024

Hom.:

AF XY:

0.00602

AC XY:

817

AN XY:

135736

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00307

Gnomad ASJ exome

AF:

0.00248

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00219

Gnomad FIN exome

AF:

0.0141

Gnomad NFE exome

AF:

0.00857

Gnomad OTH exome

AF:

0.00620

GnomAD4 exome

AF:

0.00889

AC:

12992

AN:

1461746

Hom.:

Cov.:

AF XY:

0.00879

AC XY:

6391

AN XY:

727180

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00347

Gnomad4 ASJ exome

AF:

0.00191

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00218

Gnomad4 FIN exome

AF:

0.0145

Gnomad4 NFE exome

AF:

0.0102

Gnomad4 OTH exome

AF:

0.00669

GnomAD4 genome

AF:

0.00600

AC:

913

AN:

152230

Hom.:

Cov.:

AF XY:

0.00595

AC XY:

443

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.00373

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00270

Gnomad4 FIN

AF:

0.0122

Gnomad4 NFE

AF:

0.00929

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00805

Hom.:

Bravo

AF:

0.00530

TwinsUK

AF:

0.00755

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00802

AC:

ExAC

AF:

0.00552

AC:

670

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00747

EpiControl

AF:

0.00771

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2024

IL12RB1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.054

DANN

Benign

0.64

DEOGEN2

Benign

0.16

T;T;.

Eigen

Benign

-2.0

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.0042

LIST_S2

Benign

0.61

.;T;T

MetaRNN

Benign

0.0072

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.90

L;L;L

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.67

.;.;N

REVEL

Benign

0.028

Sift4G

Benign

0.49

T;T;T

Polyphen

0.019

B;B;B

Vest4

0.042

MVP

0.23

MPC

0.097

ClinPred

0.00073

GERP RS

-8.7

Varity_R

0.013

gMVP

0.15

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over