dbSNP rs2069812: ENSG00000283782:c.-168-15060A>G (chr5-132544224-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000638452.2(ENSG00000283782):c.-168-15060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,114 control chromosomes in the GnomAD database, including 26,057 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 0.54 ( 26057 hom., cov: 32)

Consequence

ENSG00000283782
ENST00000638452.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.56

Publications

79 publications found

Variant links:

Genes affected

ENSG00000283782 (HGNC:):

ENSG00000283782 links:

IL5 (HGNC:6016): (interleukin 5) This gene encodes a cytokine that acts as a growth and differentiation factor for both B cells and eosinophils. The encoded cytokine plays a major role in the regulation of eosinophil formation, maturation, recruitment and survival. The increased production of this cytokine may be related to pathogenesis of eosinophil-dependent inflammatory diseases. This cytokine functions by binding to its receptor, which is a heterodimer, whose beta subunit is shared with the receptors for interleukine 3 (IL3) and colony stimulating factor 2 (CSF2/GM-CSF). This gene is located on chromosome 5 within a cytokine gene cluster which includes interleukin 4 (IL4), interleukin 13 (IL13), and CSF2 . This gene, IL4, and IL13 may be regulated coordinately by long-range regulatory elements spread over 120 kilobases on chromosome 5q31. [provided by RefSeq, Jul 2013]

IL5 links:

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new If you want to explore the variant's impact on the transcript ENST00000638452.2, 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-15060A>G	intron	N/A	ENSP00000492349.2	A0A1W2PQ90
ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-12108A>G	intron	N/A	ENSP00000491158.2	A0A1W2PQ90
ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-15060A>G	intron	N/A	ENSP00000491596.2	A0A1W2PQ90

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82331

AN:

151996

Hom.:

26051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.632

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.712

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.551

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

GnomAD4 genome

AF:

0.541

AC:

82341

AN:

152114

Hom.:

26057

Cov.:

AF XY:

0.546

AC XY:

40607

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.203

AC:

8435

AN:

41492

American (AMR)

AF:

0.632

AC:

9655

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.649

AC:

2250

AN:

3468

East Asian (EAS)

AF:

0.319

AC:

1646

AN:

5166

South Asian (SAS)

AF:

0.678

AC:

3266

AN:

4816

European-Finnish (FIN)

AF:

0.712

AC:

7538

AN:

10580

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.702

AC:

47719

AN:

68000

Other (OTH)

AF:

0.547

AC:

1156

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1563

3127

4690

6254

7817

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.649

Hom.:

74952

Bravo

AF:

0.511

Asia WGS

AF:

0.489

AC:

1703

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.010

(source)

DANN

Benign

0.56

PhyloP100

-1.6

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over