Genetic Variant CCL13:c.192-54G>A (chr17-34357972-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_005408.3(CCL13):c.192-54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,306,394 control chromosomes in the GnomAD database, including 178,665 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 0.47 ( 17269 hom., cov: 32)

Exomes 𝑓: 0.52 ( 161396 hom. )

Consequence

CCL13
NM_005408.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.279

Publications

4 publications found

Variant links:

Genes affected

CCL13 (HGNC:10611): (C-C motif chemokine ligand 13) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q-arm of chromosome 17. 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, lymphocytes, basophils and eosinophils, but not neutrophils. This chemokine plays a role in accumulation of leukocytes during inflammation. It may also be involved in the recruitment of monocytes into the arterial wall during artherosclerosis. [provided by RefSeq, Sep 2014]

CCL13 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005408.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL13	NM_005408.3	MANE Select	c.192-54G>A		intron	N/A	NP_005399.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL13	ENST00000225844.7	TSL:1 MANE Select	c.192-54G>A		intron	N/A	ENSP00000225844.2
	CCL13	ENST00000577681.1	TSL:1	c.84-54G>A		intron	N/A	ENSP00000463667.1

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71210

AN:

151914

Hom.:

17267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.519

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.545

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.524

AC:

604864

AN:

1154362

Hom.:

161396

AF XY:

0.526

AC XY:

309046

AN XY:

587580

show subpopulations

African (AFR)

AF:

0.337

AC:

9039

AN:

26844

American (AMR)

AF:

0.317

AC:

12256

AN:

38614

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

14455

AN:

23454

East Asian (EAS)

AF:

0.433

AC:

16515

AN:

38138

South Asian (SAS)

AF:

0.506

AC:

39409

AN:

77910

European-Finnish (FIN)

AF:

0.483

AC:

25193

AN:

52204

Middle Eastern (MID)

AF:

0.571

AC:

2023

AN:

3544

European-Non Finnish (NFE)

AF:

0.545

AC:

459864

AN:

843890

Other (OTH)

AF:

0.525

AC:

26110

AN:

49764

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

14141

28281

42422

56562

70703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11408

22816

34224

45632

57040

<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:

0.469

AC:

71230

AN:

152032

Hom.:

17269

Cov.:

AF XY:

0.466

AC XY:

34640

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.348

AC:

14422

AN:

41462

American (AMR)

AF:

0.395

AC:

6038

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2136

AN:

3470

East Asian (EAS)

AF:

0.450

AC:

2318

AN:

5156

South Asian (SAS)

AF:

0.520

AC:

2506

AN:

4822

European-Finnish (FIN)

AF:

0.479

AC:

5065

AN:

10566

Middle Eastern (MID)

AF:

0.595

AC:

175

AN:

294

European-Non Finnish (NFE)

AF:

0.545

AC:

37036

AN:

67962

Other (OTH)

AF:

0.494

AC:

1044

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1900

3800

5700

7600

9500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

668

1336

2004

2672

3340

<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:

0.512

Hom.:

30753

Bravo

AF:

0.458

Asia WGS

AF:

0.475

AC:

1652

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

9.2

(source)

DANN

Benign

0.37

PhyloP100

0.28

PromoterAI

0.0027

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over