rs1799864

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001123396.4(CCR2):c.190G>A(p.Val64Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 1,613,940 control chromosomes in the GnomAD database, including 9,257 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign,protective (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1287 hom., cov: 32)

Exomes 𝑓: 0.094 ( 7970 hom. )

Consequence

CCR2
NM_001123396.4 missense

Scores

Clinical Significance

Benign; protective no assertion criteria provided B:2

Conservation

PhyloP100: 1.13

Publications

380 publications found

Variant links:

Genes affected

CCR2 (HGNC:1603): (C-C motif chemokine receptor 2) The protein encoded by this gene is a receptor for monocyte chemoattractant protein-1, a chemokine which specifically mediates monocyte chemotaxis. Monocyte chemoattractant protein-1 is involved in monocyte infiltration in inflammatory diseases such as rheumatoid arthritis as well as in the inflammatory response against tumors. The encoded protein mediates agonist-dependent calcium mobilization and inhibition of adenylyl cyclase. This protein can also be a coreceptor with CD4 for HIV-1 infection. This gene is located in the chemokine receptor gene cluster region of chromosome 3. [provided by RefSeq, Aug 2017]

CCR2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017913282).

BP6

Variant 3-46357717-G-A is Benign according to our data. Variant chr3-46357717-G-A is described in ClinVar as Benign|protective. ClinVar VariationId is 8267.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR2	NM_001123396.4 link	c.190G>A	p.Val64Ile	missense_variant	Exon 2 of 2	ENST00000445132.3	NP_001116868.1
CCR2	NM_001123041.3 link	c.190G>A	p.Val64Ile	missense_variant	Exon 2 of 3		NP_001116513.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
CCR2	ENST00000445132.3 link	c.190G>A	p.Val64Ile	missense_variant	Exon 2 of 2	1	NM_001123396.4	ENSP00000399285.2
CCR2	ENST00000400888.2 link	c.190G>A	p.Val64Ile	missense_variant	Exon 1 of 2	1		ENSP00000383681.2
CCR2	ENST00000421659.1 link	c.190G>A	p.Val64Ile	missense_variant	Exon 3 of 3	4		ENSP00000396736.1
CCR2	ENST00000465202.1 link	n.315-400G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18420

AN:

151958

Hom.:

1285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0632

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.0900

Gnomad OTH

AF:

0.132

GnomAD2 exomes

AF:

0.127

AC:

31797

AN:

251286

AF XY:

0.121

show subpopulations

Gnomad AFR exome

AF:

0.162

Gnomad AMR exome

AF:

0.229

Gnomad ASJ exome

AF:

0.127

Gnomad EAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.0661

Gnomad NFE exome

AF:

0.0942

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.0943

AC:

137839

AN:

1461864

Hom.:

7970

Cov.:

AF XY:

0.0946

AC XY:

68798

AN XY:

727236

show subpopulations

African (AFR)

AF:

0.167

AC:

5593

AN:

33480

American (AMR)

AF:

0.223

AC:

9980

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

3141

AN:

26136

East Asian (EAS)

AF:

0.244

AC:

9677

AN:

39700

South Asian (SAS)

AF:

0.110

AC:

9474

AN:

86258

European-Finnish (FIN)

AF:

0.0710

AC:

3793

AN:

53420

Middle Eastern (MID)

AF:

0.139

AC:

801

AN:

5768

European-Non Finnish (NFE)

AF:

0.0803

AC:

89239

AN:

1111986

Other (OTH)

AF:

0.102

AC:

6141

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9110

18220

27329

36439

45549

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3380

6760

10140

13520

16900

<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:

0.121

AC:

18445

AN:

152076

Hom.:

1287

Cov.:

AF XY:

0.123

AC XY:

9115

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.157

AC:

6501

AN:

41468

American (AMR)

AF:

0.171

AC:

2617

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

434

AN:

3472

East Asian (EAS)

AF:

0.212

AC:

1098

AN:

5178

South Asian (SAS)

AF:

0.121

AC:

581

AN:

4820

European-Finnish (FIN)

AF:

0.0632

AC:

668

AN:

10566

Middle Eastern (MID)

AF:

0.164

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0900

AC:

6117

AN:

67982

Other (OTH)

AF:

0.130

AC:

274

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

786

1571

2357

3142

3928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.108

Hom.:

2176

Bravo

AF:

0.132

TwinsUK

AF:

0.0769

AC:

285

ALSPAC

AF:

0.0703

AC:

271

ESP6500AA

AF:

0.158

AC:

495

ESP6500EA

AF:

0.0920

AC:

659

ExAC

AF:

0.126

AC:

15351

Asia WGS

AF:

0.184

AC:

638

AN:

3478

EpiCase

AF:

0.0955

EpiControl

AF:

0.0912

ClinVar

Significance: Benign; protective

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CCR2-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Susceptibility to HIV infection

Benign:1

May 18, 2015

OMIM

Significance:protective

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.031

.;T;.;T

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.35

FATHMM_MKL

Benign

0.56

LIST_S2

Benign

0.69

T;T;T;.

MetaRNN

Benign

0.0018

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.78

N;N;.;N

PhyloP100

1.1

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.48

N;N;N;N

REVEL

Benign

0.030

Sift

Benign

0.33

T;T;T;T

Sift4G

Benign

0.38

T;T;T;T

Polyphen

0.079

.;B;.;B

Vest4

0.080

MPC

0.20

ClinPred

0.0028

GERP RS

1.6

PromoterAI

0.0022

Neutral

(source)

Varity_R

0.045

gMVP

0.10

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over