rs12044804

Variant names:

• chr1-206815188-A-G
• rs12044804
• NM_153758.5:c.-3+16182A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-206815188-A-G
• chr1-206815188-A-T

Variant summary

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

The NM_153758.5(IL19):​c.-3+16182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,960 control chromosomes in the GnomAD database, including 20,512 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 0.51 (20512 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 12 publications found

Genes affected

IL19 (HGNC:5990): (interleukin 19) The protein encoded by this gene is a cytokine that belongs to the IL10 cytokine subfamily. This cytokine is found to be preferentially expressed in monocytes. It can bind the IL20 receptor complex and lead to the activation of the signal transducer and activator of transcription 3 (STAT3). A similar cytokine in mouse is reported to up-regulate the expression of IL6 and TNF-alpha and induce apoptosis, which suggests a role of this cytokine in inflammatory responses. Alternatively spliced transcript variants encoding the distinct isoforms have been described. [provided by RefSeq, Jul 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.-3+16182A>G		intron_variant	Intron 2 of 6	ENST00000659997.3	NP_715639.2
IL19	NM_001393490.1	c.-3+16182A>G		intron_variant	Intron 2 of 6		NP_001380419.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3	c.-3+16182A>G		intron_variant	Intron 2 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-3+16182A>G		intron_variant	Intron 2 of 6			ENSP00000499487.2
IL19	ENST00000662320.1	n.214-10302A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78082 AN: 151842 Hom.: 20491 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.514 AC: 78137 AN: 151960 Hom.: 20512 Cov.: 31 AF XY: 0.515 AC XY: 38266 AN XY: 74270

African (AFR) AF: 0.501 AC: 20743 AN: 41412

American (AMR) AF: 0.558 AC: 8530 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4587 AN: 5176

South Asian (SAS) AF: 0.393 AC: 1892 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 4998 AN: 10552

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34319 AN: 67940

Other (OTH) AF: 0.488 AC: 1031 AN: 2114

Alfa AF: 0.499 Hom.: 32216

Bravo AF: 0.523

Asia WGS AF: 0.591 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		0.32
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: rs12044804; hg19: chr1-206988533;