1-206778859-C-G

Variant names:

• chr1-206778859-C-G
• rs10494879
• NM_153758.5:c.-149+7781C>G

Variant summary

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

The NM_153758.5(IL19):​c.-149+7781C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,082 control chromosomes in the GnomAD database, including 10,242 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 0.36 (10242 hom., cov: 32)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 21 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153758.5. 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
	IL19	NM_153758.5	MANE Select	c.-149+7781C>G		intron	N/A	NP_715639.2	Q9UHD0-1
	IL19	NM_001393490.1		c.-149+8029C>G		intron	N/A	NP_001380419.1	Q9UHD0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.-149+7781C>G		intron	N/A	ENSP00000499459.2	Q9UHD0-1
	IL19	ENST00000656872.2		c.-149+8029C>G		intron	N/A	ENSP00000499487.2	Q9UHD0-1
	IL19	ENST00000662320.1		n.67+8029C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54047 AN: 151962 Hom.: 10219 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.356 AC: 54108 AN: 152082 Hom.: 10242 Cov.: 32 AF XY: 0.349 AC XY: 25924 AN XY: 74344

African (AFR) AF: 0.332 AC: 13742 AN: 41448

American (AMR) AF: 0.251 AC: 3839 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3470

East Asian (EAS) AF: 0.0524 AC: 272 AN: 5192

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4824

European-Finnish (FIN) AF: 0.407 AC: 4308 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28524 AN: 67960

Other (OTH) AF: 0.332 AC: 702 AN: 2112

Alfa AF: 0.387 Hom.: 1431

Bravo AF: 0.344

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.26
PhyloP100		1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10494879; hg19: chr1-206952204;