Genetic Variant CCL22:c.*1849G>A (chr16-57365437-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002990.5(CCL22):c.*1849G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,312 control chromosomes in the GnomAD database, including 60,477 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 0.89 ( 60435 hom., cov: 32)

Exomes 𝑓: 0.94 ( 42 hom. )

Consequence

CCL22
NM_002990.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.460

Publications

5 publications found

Variant links:

Genes affected

CCL22 (HGNC:10621): (C-C motif chemokine ligand 22) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 16. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for monocytes, dendritic cells, natural killer cells and for chronically activated T lymphocytes. It also displays a mild activity for primary activated T lymphocytes and has no chemoattractant activity for neutrophils, eosinophils and resting T lymphocytes. The product of this gene binds to chemokine receptor CCR4. This chemokine may play a role in the trafficking of activated T lymphocytes to inflammatory sites and other aspects of activated T lymphocyte physiology. [provided by RefSeq, Sep 2014]

CCL22 links:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCL22	NM_002990.5 link	c.*1849G>A	3_prime_UTR_variant	Exon 3 of 3	ENST00000219235.5	NP_002981.2	O00626
CCL22	XM_047434449.1 link	c.*1849G>A	3_prime_UTR_variant	Exon 4 of 4		XP_047290405.1
CCL22	XM_047434450.1 link	c.*1849G>A	3_prime_UTR_variant	Exon 4 of 4		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5 link	c.*1849G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_002990.5	ENSP00000219235.4		O00626

Frequencies

GnomAD3 genomes

AF:

0.889

AC:

135243

AN:

152098

Hom.:

60407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.848

Gnomad AMI

AF:

0.860

Gnomad AMR

AF:

0.812

Gnomad ASJ

AF:

0.946

Gnomad EAS

AF:

0.712

Gnomad SAS

AF:

0.877

Gnomad FIN

AF:

0.919

Gnomad MID

AF:

0.845

Gnomad NFE

AF:

0.939

Gnomad OTH

AF:

0.899

GnomAD4 exome

AF:

0.938

AC:

AN:

Hom.:

Cov.:

AF XY:

0.931

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.949

AC:

AN:

Other (OTH)

AF:

0.800

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.889

AC:

135322

AN:

152216

Hom.:

60435

Cov.:

AF XY:

0.885

AC XY:

65893

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.847

AC:

35171

AN:

41506

American (AMR)

AF:

0.812

AC:

12408

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.946

AC:

3281

AN:

3468

East Asian (EAS)

AF:

0.711

AC:

3677

AN:

5168

South Asian (SAS)

AF:

0.877

AC:

4229

AN:

4820

European-Finnish (FIN)

AF:

0.919

AC:

9763

AN:

10620

Middle Eastern (MID)

AF:

0.844

AC:

248

AN:

294

European-Non Finnish (NFE)

AF:

0.939

AC:

63855

AN:

68030

Other (OTH)

AF:

0.901

AC:

1906

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

758

1515

2273

3030

3788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

902

1804

2706

3608

4510

<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:

0.911

Hom.:

29317

Bravo

AF:

0.876

Asia WGS

AF:

0.783

AC:

2726

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.2

(source)

DANN

Benign

0.54

PhyloP100

0.46

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over