rs2243188

Variant names:

• chr1-206841127-A-C
• rs2243188
• NM_153758.5:c.438+49A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-206841127-A-C
• chr1-206841127-A-G
• chr1-206841127-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.438+49A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,485,528 control chromosomes in the GnomAD database, including 407,337 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 0.69 (37090 hom., cov: 32)
  • Exomes 𝑓: 0.74 (370247 hom.)
• Consequence: IL19 NM_153758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 38 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]

LOC105372878 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL19	NM_153758.5	c.438+49A>C		intron_variant	Intron 6 of 6	ENST00000659997.3	NP_715639.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL19	ENST00000659997.3	c.438+49A>C		intron_variant	Intron 6 of 6		NM_153758.5	ENSP00000499459.2
IL19	ENST00000270218.10	c.438+49A>C		intron_variant	Intron 6 of 6	1		ENSP00000270218.6
IL19	ENST00000340758.7	c.438+49A>C		intron_variant	Intron 5 of 5	1		ENSP00000343000.3
IL19	ENST00000656872.2	c.438+49A>C		intron_variant	Intron 6 of 6			ENSP00000499487.2

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104911 AN: 152010 Hom.: 37049 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.700

GnomAD2 exomes AF: 0.690 AC: 171225 AN: 248016 AF XY: 0.698

Gnomad AFR exome AF: 0.587

Gnomad AMR exome AF: 0.605

Gnomad ASJ exome AF: 0.789

Gnomad EAS exome AF: 0.384

Gnomad FIN exome AF: 0.720

Gnomad NFE exome AF: 0.763

Gnomad OTH exome AF: 0.721

GnomAD4 exome AF: 0.741 AC: 987459 AN: 1333400 Hom.: 370247 Cov.: 19 AF XY: 0.740 AC XY: 495739 AN XY: 670050

African (AFR) AF: 0.592 AC: 18241 AN: 30822

American (AMR) AF: 0.610 AC: 27037 AN: 44288

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 19968 AN: 25320

East Asian (EAS) AF: 0.362 AC: 14133 AN: 39034

South Asian (SAS) AF: 0.693 AC: 57856 AN: 83432

European-Finnish (FIN) AF: 0.719 AC: 38229 AN: 53200

Middle Eastern (MID) AF: 0.687 AC: 3803 AN: 5532

European-Non Finnish (NFE) AF: 0.771 AC: 767687 AN: 995824

Other (OTH) AF: 0.724 AC: 40505 AN: 55948

GnomAD4 genome AF: 0.690 AC: 105005 AN: 152128 Hom.: 37090 Cov.: 32 AF XY: 0.685 AC XY: 50946 AN XY: 74356

African (AFR) AF: 0.590 AC: 24478 AN: 41510

American (AMR) AF: 0.663 AC: 10127 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2735 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2061 AN: 5170

South Asian (SAS) AF: 0.682 AC: 3285 AN: 4816

European-Finnish (FIN) AF: 0.721 AC: 7632 AN: 10580

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52347 AN: 67988

Other (OTH) AF: 0.701 AC: 1478 AN: 2108

Alfa AF: 0.699 Hom.: 12193

Bravo AF: 0.674

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.23
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: rs2243188; hg19: chr1-207014472; COSMIC: COSV54282946; COSMIC: COSV54282946;