5-159325970-A-T

Position:

• chr5-159325970-A-T

Variant summary

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

The NM_002187.3(IL12B):​c.88+725T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,080 control chromosomes in the GnomAD database, including 6,391 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 0.28 (6391 hom., cov: 32)
• Consequence: IL12B NM_002187.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437

Genes affected

IL12B (HGNC:5970): (interleukin 12B) This gene encodes a subunit of interleukin 12, a cytokine that acts on T and natural killer cells, and has a broad array of biological activities. Interleukin 12 is a disulfide-linked heterodimer composed of the 40 kD cytokine receptor like subunit encoded by this gene, and a 35 kD subunit encoded by IL12A. This cytokine is expressed by activated macrophages that serve as an essential inducer of Th1 cells development. This cytokine has been found to be important for sustaining a sufficient number of memory/effector Th1 cells to mediate long-term protection to an intracellular pathogen. Overexpression of this gene was observed in the central nervous system of patients with multiple sclerosis (MS), suggesting a role of this cytokine in the pathogenesis of the disease. The promoter polymorphism of this gene has been reported to be associated with the severity of atopic and non-atopic asthma in children. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12B	NM_002187.3	c.88+725T>A		intron_variant		ENST00000231228.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12B	ENST00000231228.3	c.88+725T>A		intron_variant		1	NM_002187.3	P1
IL12B	ENST00000696750.1	c.-149+4462T>A		intron_variant
IL12B	ENST00000696751.1	c.88+725T>A		intron_variant, NMD_transcript_variant
	ENST00000521472.6	n.410+316A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43208 AN: 151962 Hom.: 6393 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.284 AC: 43211 AN: 152080 Hom.: 6391 Cov.: 32 AF XY: 0.285 AC XY: 21208 AN XY: 74322

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.250

Alfa AF: 0.307 Hom.: 978

Bravo AF: 0.272

Asia WGS AF: 0.269 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.72

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: rs3181216; hg19: chr5-158752978;