dbSNP rs2287936: CCL25:c.*222G>A (chr19-8062447-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_005624.4(CCL25):c.*222G>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 0.0888 in 567,768 control chromosomes in the GnomAD database, including 2,697 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 0.081 ( 692 hom., cov: 32)

Exomes 𝑓: 0.092 ( 2005 hom. )

Consequence

CCL25
NM_005624.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.518

Publications

9 publications found

Variant links:

Genes affected

CCL25 (HGNC:10624): (C-C motif chemokine ligand 25) This antimicrobial gene belongs to the subfamily of small cytokine CC genes. 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 dendritic cells, thymocytes, and activated macrophages but is inactive on peripheral blood lymphocytes and neutrophils. The product of this gene binds to chemokine receptor CCR9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

CCL25 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL25	NM_005624.4 link	c.*222G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000315626.6	NP_005615.2	O15444-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL25	ENST00000315626.6 link	c.*222G>A		3_prime_UTR_variant	Exon 6 of 6	2	NM_005624.4	ENSP00000324756.6		O15444-1C9JDZ7

Frequencies

GnomAD3 genomes

AF:

0.0813

AC:

12361

AN:

152018

Hom.:

685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0213

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.0744

Gnomad EAS

AF:

0.0825

Gnomad SAS

AF:

0.0886

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.0417

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.0834

GnomAD4 exome

AF:

0.0915

AC:

38032

AN:

415632

Hom.:

2005

Cov.:

AF XY:

0.0916

AC XY:

19991

AN XY:

218340

show subpopulations

African (AFR)

AF:

0.0259

AC:

305

AN:

11754

American (AMR)

AF:

0.185

AC:

3276

AN:

17742

Ashkenazi Jewish (ASJ)

AF:

0.0644

AC:

827

AN:

12844

East Asian (EAS)

AF:

0.103

AC:

2996

AN:

29222

South Asian (SAS)

AF:

0.0945

AC:

4020

AN:

42540

European-Finnish (FIN)

AF:

0.132

AC:

3569

AN:

26986

Middle Eastern (MID)

AF:

0.0462

AC:

AN:

1820

European-Non Finnish (NFE)

AF:

0.0841

AC:

20902

AN:

248656

Other (OTH)

AF:

0.0853

AC:

2053

AN:

24068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1532

3064

4596

6128

7660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

320

480

640

800

<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:

0.0814

AC:

12381

AN:

152136

Hom.:

692

Cov.:

AF XY:

0.0847

AC XY:

6301

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0213

AC:

886

AN:

41552

American (AMR)

AF:

0.172

AC:

2626

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.0744

AC:

258

AN:

3470

East Asian (EAS)

AF:

0.0823

AC:

425

AN:

5166

South Asian (SAS)

AF:

0.0889

AC:

429

AN:

4824

European-Finnish (FIN)

AF:

0.146

AC:

1545

AN:

10570

Middle Eastern (MID)

AF:

0.0448

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0872

AC:

5928

AN:

68006

Other (OTH)

AF:

0.0825

AC:

174

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

556

1113

1669

2226

2782

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0829

Hom.:

1053

Bravo

AF:

0.0814

Asia WGS

AF:

0.0940

AC:

327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.5

(source)

DANN

Benign

0.57

PhyloP100

-0.52

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