Variant rs2032887 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005624.4(CCL25):c.302A>G(p.His101Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,613,704 control chromosomes in the GnomAD database, including 46,101 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.25 ( 4906 hom., cov: 33)

Exomes 𝑓: 0.23 ( 41195 hom. )

Consequence

CCL25
NM_005624.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004403174).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL25	NM_005624.4 linkuse as main transcript	c.302A>G	p.His101Arg	missense_variant	4/6	ENST00000315626.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL25	ENST00000315626.6 linkuse as main transcript	c.302A>G	p.His101Arg	missense_variant	4/6	2	NM_005624.4	A1	O15444-1

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37960

AN:

152036

Hom.:

4889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.459

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.237

AC:

59020

AN:

248944

Hom.:

7329

AF XY:

0.234

AC XY:

31648

AN XY:

135180

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.304

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.0970

Gnomad SAS exome

AF:

0.191

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.235

AC:

343118

AN:

1461550

Hom.:

41195

Cov.:

AF XY:

0.234

AC XY:

170087

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.256

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.252

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.285

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.250

AC:

38021

AN:

152154

Hom.:

4906

Cov.:

AF XY:

0.250

AC XY:

18588

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.260

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.104

Gnomad4 SAS

AF:

0.178

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.233

Hom.:

7595

Bravo

AF:

0.254

TwinsUK

AF:

0.234

AC:

868

ALSPAC

AF:

0.234

AC:

900

ESP6500AA

AF:

0.247

AC:

1023

ESP6500EA

AF:

0.243

AC:

2044

ExAC

AF:

0.231

AC:

27992

Asia WGS

AF:

0.162

AC:

562

AN:

3478

EpiCase

AF:

0.237

EpiControl

AF:

0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.048

BayesDel_addAF

Benign

-0.87

BayesDel_noAF

Benign

-0.88

Cadd

Benign

0.0030

Dann

Benign

0.13

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0060

LIST_S2

Benign

0.20

T;T;T

MetaRNN

Benign

0.0044

T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.46

N;N;.

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.20

PROVEAN

Benign

-1.7

N;N;.

REVEL

Benign

0.024

Sift

Benign

0.50

T;T;.

Sift4G

Benign

0.35

T;T;T

Polyphen

0.0

.;B;.

Vest4

0.022

MPC

0.44

ClinPred

0.0022

GERP RS

-3.0

Varity_R

0.035

gMVP

0.097

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over