dbSNP rs11080369: CCL16:c.197+15T>G (chr17-35978128-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004590.4(CCL16):c.197+15T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 1,613,960 control chromosomes in the GnomAD database, including 5,258 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 0.093 ( 771 hom., cov: 32)

Exomes 𝑓: 0.074 ( 4487 hom. )

Consequence

CCL16
NM_004590.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459

Publications

20 publications found

Variant links:

Genes affected

CCL16 (HGNC:10614): (C-C motif chemokine ligand 16) This gene is one of several 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 lymphocytes and monocytes but not for neutrophils. This cytokine also shows a potent myelosuppressive activity and suppresses proliferation of myeloid progenitor cells. The expression of this gene is upregulated by IL-10. [provided by RefSeq, Jul 2008]

CCL16 links:

ENSG00000270240 (HGNC:):

ENSG00000270240 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL16	NM_004590.4 link	c.197+15T>G		intron_variant	Intron 2 of 2	ENST00000611905.2	NP_004581.1	O15467

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL16	ENST00000611905.2 link	c.197+15T>G		intron_variant	Intron 2 of 2	1	NM_004590.4	ENSP00000478024.1		O15467

Frequencies

GnomAD3 genomes

AF:

0.0931

AC:

14151

AN:

152064

Hom.:

767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.0636

Gnomad SAS

AF:

0.0552

Gnomad FIN

AF:

0.0512

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0685

Gnomad OTH

AF:

0.0798

GnomAD2 exomes

AF:

0.0837

AC:

21046

AN:

251418

AF XY:

0.0769

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.184

Gnomad ASJ exome

AF:

0.0435

Gnomad EAS exome

AF:

0.0594

Gnomad FIN exome

AF:

0.0498

Gnomad NFE exome

AF:

0.0684

Gnomad OTH exome

AF:

0.0670

GnomAD4 exome

AF:

0.0740

AC:

108165

AN:

1461778

Hom.:

4487

Cov.:

AF XY:

0.0723

AC XY:

52603

AN XY:

727202

show subpopulations

African (AFR)

AF:

0.140

AC:

4688

AN:

33474

American (AMR)

AF:

0.178

AC:

7943

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0406

AC:

1061

AN:

26134

East Asian (EAS)

AF:

0.0526

AC:

2088

AN:

39700

South Asian (SAS)

AF:

0.0533

AC:

4599

AN:

86258

European-Finnish (FIN)

AF:

0.0490

AC:

2618

AN:

53416

Middle Eastern (MID)

AF:

0.0718

AC:

414

AN:

5768

European-Non Finnish (NFE)

AF:

0.0722

AC:

80326

AN:

1111916

Other (OTH)

AF:

0.0733

AC:

4428

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

5137

10274

15412

20549

25686

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3140

6280

9420

12560

15700

<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:

0.0931

AC:

14168

AN:

152182

Hom.:

771

Cov.:

AF XY:

0.0937

AC XY:

6973

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.142

AC:

5914

AN:

41514

American (AMR)

AF:

0.137

AC:

2094

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0421

AC:

146

AN:

3470

East Asian (EAS)

AF:

0.0632

AC:

327

AN:

5176

South Asian (SAS)

AF:

0.0557

AC:

268

AN:

4814

European-Finnish (FIN)

AF:

0.0512

AC:

542

AN:

10592

Middle Eastern (MID)

AF:

0.0411

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0685

AC:

4657

AN:

68008

Other (OTH)

AF:

0.0822

AC:

174

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

655

1311

1966

2622

3277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.0769

Hom.:

1506

Bravo

AF:

0.103

Asia WGS

AF:

0.0790

AC:

274

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.6

(source)

DANN

Benign

0.65

PhyloP100

-0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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