chr1-206834296-C-G

Position:

• chr1-206834296-C-G

Variant summary

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

The NM_013371.5(IL19):​c.-107C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 985,412 control chromosomes in the GnomAD database, including 404,556 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 0.89 (59925 hom., cov: 32)
  • Exomes 𝑓: 0.91 (344631 hom.)
• Consequence: IL19 NM_013371.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL19	NM_153758.5	c.-2-2365C>G		intron_variant		ENST00000659997.3	NP_715639.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000270218.10	c.-107C>G		5_prime_UTR_variant	2/7	1		ENSP00000270218.6
IL19	ENST00000659997.3	c.-2-2365C>G		intron_variant			NM_153758.5	ENSP00000499459.2
IL19	ENST00000656872.2	c.-2-2365C>G		intron_variant				ENSP00000499487.2

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134844 AN: 152138 Hom.: 59867 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.890

GnomAD4 exome AF: 0.909 AC: 757719 AN: 833156 Hom.: 344631 Cov.: 36 AF XY: 0.910 AC XY: 350079 AN XY: 384752

Gnomad4 AFR exome AF: 0.856

Gnomad4 AMR exome AF: 0.881

Gnomad4 ASJ exome AF: 0.914

Gnomad4 EAS exome AF: 0.803

Gnomad4 SAS exome AF: 0.920

Gnomad4 FIN exome AF: 0.878

Gnomad4 NFE exome AF: 0.911

Gnomad4 OTH exome AF: 0.903

GnomAD4 genome AF: 0.886 AC: 134960 AN: 152256 Hom.: 59925 Cov.: 32 AF XY: 0.885 AC XY: 65856 AN XY: 74420

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.890

Alfa AF: 0.900 Hom.: 29573

Bravo AF: 0.879

Asia WGS AF: 0.833 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	12
DANN	Benign	0.78

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: rs2243158; hg19: chr1-207007641;