dbSNP rs2243188: IL19:c.438+49A>C (chr1-206841127-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

38 publications found

Variant links:

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]

IL19 links:

LOC105372878 (HGNC:):

LOC105372878 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_153758.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL19	NM_153758.5	MANE Select	c.438+49A>C	intron	N/A	NP_715639.2	Q9UHD0-1
IL19	NM_001369605.1		c.438+49A>C	intron	N/A	NP_001356534.1	Q9UHD0-1
IL19	NM_001393490.1		c.438+49A>C	intron	N/A	NP_001380419.1	Q9UHD0-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL19	ENST00000659997.3	MANE Select	c.438+49A>C	intron	N/A	ENSP00000499459.2	Q9UHD0-1
IL19	ENST00000270218.10	TSL:1	c.438+49A>C	intron	N/A	ENSP00000270218.6	Q9UHD0-1
IL19	ENST00000340758.7	TSL:1	c.438+49A>C	intron	N/A	ENSP00000343000.3	Q9UHD0-1

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104911

AN:

152010

Hom.:

37049

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.740

AC XY:

495739

AN XY:

670050

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

12344

24689

37033

49378

61722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17404

34808

52212

69616

87020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.690

AC:

105005

AN:

152128

Hom.:

37090

Cov.:

AF XY:

0.685

AC XY:

50946

AN XY:

74356

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1596

3193

4789

6386

7982

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.58

PhyloP100

-0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over