dbSNP rs3138042: CCR2:c.*931A>G (chr3-46359541-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001123396.4(CCR2):c.*931A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,043,916 control chromosomes in the GnomAD database, including 51,376 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 0.32 ( 7817 hom., cov: 32)

Exomes 𝑓: 0.31 ( 43559 hom. )

Consequence

CCR2
NM_001123396.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.51

Publications

7 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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCR2	NM_001123396.4 link	c.*931A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000445132.3	NP_001116868.1	P41597-2A0A024R2Q0
CCR2	NM_001123041.3 link	c.942-136A>G		intron_variant	Intron 2 of 2		NP_001116513.2	P41597-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR2	ENST00000445132.3 link	c.*931A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001123396.4	ENSP00000399285.2		P41597-2
CCR2	ENST00000400888.2 link	c.942-136A>G		intron_variant	Intron 1 of 1	1		ENSP00000383681.2		P41597-1

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48561

AN:

151798

Hom.:

7800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.313

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.337

GnomAD4 exome

AF:

0.309

AC:

275829

AN:

892002

Hom.:

43559

Cov.:

AF XY:

0.311

AC XY:

138647

AN XY:

445868

show subpopulations

African (AFR)

AF:

0.332

AC:

6876

AN:

20694

American (AMR)

AF:

0.322

AC:

5582

AN:

17318

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

4319

AN:

16466

East Asian (EAS)

AF:

0.270

AC:

8988

AN:

33326

South Asian (SAS)

AF:

0.366

AC:

19659

AN:

53784

European-Finnish (FIN)

AF:

0.288

AC:

10219

AN:

35456

Middle Eastern (MID)

AF:

0.387

AC:

1093

AN:

2822

European-Non Finnish (NFE)

AF:

0.307

AC:

206249

AN:

671834

Other (OTH)

AF:

0.319

AC:

12844

AN:

40302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

9143

18286

27429

36572

45715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5964

11928

17892

23856

29820

<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:

0.320

AC:

48596

AN:

151914

Hom.:

7817

Cov.:

AF XY:

0.322

AC XY:

23921

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.332

AC:

13733

AN:

41414

American (AMR)

AF:

0.353

AC:

5396

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

934

AN:

3470

East Asian (EAS)

AF:

0.312

AC:

1609

AN:

5154

South Asian (SAS)

AF:

0.355

AC:

1711

AN:

4820

European-Finnish (FIN)

AF:

0.291

AC:

3066

AN:

10546

Middle Eastern (MID)

AF:

0.377

AC:

110

AN:

292

European-Non Finnish (NFE)

AF:

0.310

AC:

21057

AN:

67928

Other (OTH)

AF:

0.334

AC:

706

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1676

3352

5027

6703

8379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.307

Hom.:

2468

Bravo

AF:

0.323

Asia WGS

AF:

0.309

AC:

1073

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.4

(source)

DANN

Benign

0.44

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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