1-206783747-C-A

Variant names:

• chr1-206783747-C-A
• rs6667202
• NM_153758.5:c.-149+12669C>A

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+12669C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,010 control chromosomes in the GnomAD database, including 27,989 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 0.60 (27989 hom., cov: 31)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 24 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	NM_153758.5	MANE Select	c.-149+12669C>A		intron	N/A	NP_715639.2
	IL19	NM_001393490.1		c.-149+12917C>A		intron	N/A	NP_001380419.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL19	ENST00000659997.3	MANE Select	c.-149+12669C>A		intron	N/A	ENSP00000499459.2
	IL19	ENST00000656872.2		c.-149+12917C>A		intron	N/A	ENSP00000499487.2
	IL19	ENST00000662320.1		n.67+12917C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90491 AN: 151892 Hom.: 27977 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.596 AC: 90524 AN: 152010 Hom.: 27989 Cov.: 31 AF XY: 0.605 AC XY: 44936 AN XY: 74308

African (AFR) AF: 0.481 AC: 19911 AN: 41436

American (AMR) AF: 0.743 AC: 11354 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2496 AN: 3468

East Asian (EAS) AF: 0.973 AC: 5042 AN: 5180

South Asian (SAS) AF: 0.780 AC: 3759 AN: 4822

European-Finnish (FIN) AF: 0.578 AC: 6104 AN: 10560

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39749 AN: 67946

Other (OTH) AF: 0.640 AC: 1350 AN: 2108

Alfa AF: 0.600 Hom.: 74784

Bravo AF: 0.602

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.69
DANN	Benign	0.65
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6667202; hg19: chr1-206957092; COSMIC: COSV60019528;