Genetic Variant NM_002990.5:c.*1206_*1207insT (chr16-57364794-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002990.5(CCL22):c.*1206_*1207insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.85 ( 46914 hom., cov: 19)

Exomes 𝑓: 0.94 ( 107 hom. )

Consequence

CCL22
NM_002990.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.948

Publications

1 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
CCL22	NM_002990.5 link	c.1206_1207insT	3_prime_UTR_variant	Exon 3 of 3	ENST00000219235.5	NP_002981.2
CCL22	XM_047434449.1 link	c.1206_1207insT	3_prime_UTR_variant	Exon 4 of 4		XP_047290405.1
CCL22	XM_047434450.1 link	c.1206_1207insT	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.1206_1207insT		3_prime_UTR_variant	Exon 3 of 3	1	NM_002990.5	ENSP00000219235.4

Frequencies

GnomAD3 genomes

AF:

0.854

AC:

111741

AN:

130828

Hom.:

46913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.762

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.833

Gnomad ASJ

AF:

0.899

Gnomad EAS

AF:

0.852

Gnomad SAS

AF:

0.815

Gnomad FIN

AF:

0.932

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.898

Gnomad OTH

AF:

0.865

GnomAD4 exome

AF:

0.937

AC:

223

AN:

238

Hom.:

107

Cov.:

AF XY:

0.946

AC XY:

174

AN XY:

184

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.667

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.943

AC:

181

AN:

192

Other (OTH)

AF:

0.857

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.714

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:

0.854

AC:

111756

AN:

130858

Hom.:

46914

Cov.:

AF XY:

0.854

AC XY:

53490

AN XY:

62638

show subpopulations

African (AFR)

AF:

0.762

AC:

25264

AN:

33148

American (AMR)

AF:

0.833

AC:

10715

AN:

12868

Ashkenazi Jewish (ASJ)

AF:

0.899

AC:

2966

AN:

3300

East Asian (EAS)

AF:

0.853

AC:

3729

AN:

4374

South Asian (SAS)

AF:

0.815

AC:

3094

AN:

3798

European-Finnish (FIN)

AF:

0.932

AC:

7064

AN:

7576

Middle Eastern (MID)

AF:

0.840

AC:

200

AN:

238

European-Non Finnish (NFE)

AF:

0.898

AC:

56519

AN:

62926

Other (OTH)

AF:

0.866

AC:

1594

AN:

1840

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.623

Heterozygous variant carriers

584

1168

1753

2337

2921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.95

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

NM_002990.5:c.1206_1207insT

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