Genetic Variant CCL22:c.*2138G>A (chr16-57365726-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.*2138G>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 0.535 in 152,296 control chromosomes in the GnomAD database, including 23,939 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 0.53 ( 23885 hom., cov: 32)

Exomes 𝑓: 0.64 ( 54 hom. )

Consequence

CCL22
NM_002990.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.236

Publications

6 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCL22	NM_002990.5 link	c.*2138G>A	3_prime_UTR_variant	Exon 3 of 3	ENST00000219235.5	NP_002981.2	O00626
CCL22	XM_047434449.1 link	c.*2138G>A	3_prime_UTR_variant	Exon 4 of 4		XP_047290405.1
CCL22	XM_047434450.1 link	c.*2138G>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.*2138G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_002990.5	ENSP00000219235.4		O00626

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

81292

AN:

151918

Hom.:

23881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.570

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.694

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.710

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.578

GnomAD4 exome

AF:

0.642

AC:

167

AN:

260

Hom.:

Cov.:

AF XY:

0.654

AC XY:

123

AN XY:

188

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.333

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.662

AC:

155

AN:

234

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

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:

0.535

AC:

81321

AN:

152036

Hom.:

23885

Cov.:

AF XY:

0.534

AC XY:

39723

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.286

AC:

11873

AN:

41462

American (AMR)

AF:

0.547

AC:

8354

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.694

AC:

2403

AN:

3464

East Asian (EAS)

AF:

0.546

AC:

2813

AN:

5150

South Asian (SAS)

AF:

0.430

AC:

2070

AN:

4814

European-Finnish (FIN)

AF:

0.710

AC:

7510

AN:

10582

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.653

AC:

44398

AN:

67968

Other (OTH)

AF:

0.580

AC:

1225

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1752

3503

5255

7006

8758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<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:

0.613

Hom.:

10092

Bravo

AF:

0.515

Asia WGS

AF:

0.434

AC:

1508

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.32

PhyloP100

-0.24

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