NM_001374259.2:c.2046+210A>G

Variant names:

• chr1-67390338-A-G
• rs2270614
• NM_001374259.2:c.2046+210A>G

Variant summary

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

The NM_001374259.2(IL12RB2):​c.2046+210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,966 control chromosomes in the GnomAD database, including 18,777 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.47 (18777 hom., cov: 31)
• Consequence: IL12RB2 NM_001374259.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 12 publications found

Genes affected

IL12RB2 (HGNC:5972): (interleukin 12 receptor subunit beta 2) The protein encoded by this gene is a type I transmembrane protein identified as a subunit of the interleukin 12 receptor complex. The coexpression of this and IL12RB1 proteins was shown to lead to the formation of high-affinity IL12 binding sites and reconstitution of IL12 dependent signaling. The expression of this gene is up-regulated by interferon gamma in Th1 cells, and plays a role in Th1 cell differentiation. The up-regulation of this gene is found to be associated with a number of infectious diseases, such as Crohn's disease and leprosy, which is thought to contribute to the inflammatory response and host defense. Several transcript variants encoding different isoforms and non-protein coding transcripts have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001374259.2. 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
	IL12RB2	NM_001374259.2	MANE Select	c.2046+210A>G		intron	N/A	NP_001361188.1	Q99665-1
	IL12RB2	NM_001559.3		c.2046+210A>G		intron	N/A	NP_001550.1	Q99665-1
	IL12RB2	NM_001258215.1		c.1788+210A>G		intron	N/A	NP_001245144.1	Q99665-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12RB2	ENST00000674203.2	MANE Select	c.2046+210A>G		intron	N/A	ENSP00000501329.1	Q99665-1
	IL12RB2	ENST00000262345.5	TSL:1	c.2046+210A>G		intron	N/A	ENSP00000262345.1	Q99665-1
	IL12RB2	ENST00000544434.5	TSL:1	c.1788+210A>G		intron	N/A	ENSP00000442443.1	Q99665-3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71022 AN: 151848 Hom.: 18775 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.467 AC: 71034 AN: 151966 Hom.: 18777 Cov.: 31 AF XY: 0.473 AC XY: 35153 AN XY: 74250

African (AFR) AF: 0.229 AC: 9506 AN: 41454

American (AMR) AF: 0.465 AC: 7094 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1770 AN: 5170

South Asian (SAS) AF: 0.563 AC: 2706 AN: 4808

European-Finnish (FIN) AF: 0.693 AC: 7310 AN: 10542

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39535 AN: 67938

Other (OTH) AF: 0.446 AC: 941 AN: 2108

Alfa AF: 0.549 Hom.: 13683

Bravo AF: 0.435

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.26
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: rs2270614; hg19: chr1-67856021; COSMIC: COSV52022107;