dbSNP rs2074543: CCL22:c.73+15C>A (chr16-57358904-C-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.73+15C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 1,605,500 control chromosomes in the GnomAD database, including 2,211 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 0.026 ( 176 hom., cov: 32)

Exomes 𝑓: 0.023 ( 2035 hom. )

Consequence

CCL22
NM_002990.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Publications

7 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:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCL22	NM_002990.5 link	c.73+15C>A	intron_variant	Intron 1 of 2	ENST00000219235.5	NP_002981.2	O00626
CCL22	XM_047434449.1 link	c.112+15C>A	intron_variant	Intron 2 of 3		XP_047290405.1
CCL22	XM_047434450.1 link	c.73+15C>A	intron_variant	Intron 2 of 3		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5 link	c.73+15C>A		intron_variant	Intron 1 of 2	1	NM_002990.5	ENSP00000219235.4		O00626

Frequencies

GnomAD3 genomes

AF:

0.0258

AC:

3923

AN:

152192

Hom.:

178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0103

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0508

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.0215

Gnomad FIN

AF:

0.0349

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0325

GnomAD2 exomes

AF:

0.0396

AC:

9955

AN:

251084

AF XY:

0.0370

show subpopulations

Gnomad AFR exome

AF:

0.0108

Gnomad AMR exome

AF:

0.0708

Gnomad ASJ exome

AF:

0.0115

Gnomad EAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.0349

Gnomad NFE exome

AF:

0.0150

Gnomad OTH exome

AF:

0.0365

GnomAD4 exome

AF:

0.0234

AC:

33993

AN:

1453190

Hom.:

2035

Cov.:

AF XY:

0.0233

AC XY:

16829

AN XY:

723422

show subpopulations

African (AFR)

AF:

0.0115

AC:

382

AN:

33312

American (AMR)

AF:

0.0667

AC:

2980

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.00913

AC:

238

AN:

26072

East Asian (EAS)

AF:

0.289

AC:

11464

AN:

39626

South Asian (SAS)

AF:

0.0180

AC:

1547

AN:

86052

European-Finnish (FIN)

AF:

0.0321

AC:

1710

AN:

53296

Middle Eastern (MID)

AF:

0.0470

AC:

231

AN:

4910

European-Non Finnish (NFE)

AF:

0.0125

AC:

13832

AN:

1105202

Other (OTH)

AF:

0.0268

AC:

1609

AN:

60020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

1407

2814

4220

5627

7034

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.0257

AC:

3920

AN:

152310

Hom.:

176

Cov.:

AF XY:

0.0279

AC XY:

2080

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0105

AC:

437

AN:

41574

American (AMR)

AF:

0.0505

AC:

773

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00778

AC:

AN:

3470

East Asian (EAS)

AF:

0.228

AC:

1180

AN:

5184

South Asian (SAS)

AF:

0.0207

AC:

100

AN:

4828

European-Finnish (FIN)

AF:

0.0349

AC:

370

AN:

10616

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0139

AC:

946

AN:

68014

Other (OTH)

AF:

0.0317

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

178

357

535

714

892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0129

Hom.:

Bravo

AF:

0.0291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.092

(source)

DANN

Benign

0.69

PhyloP100

-1.7

PromoterAI

-0.012

Neutral

(source)

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