Variant 3-46357683-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001123396.4(CCR2):c.156G>T(p.Val52Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00884 in 1,614,122 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0070 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0090 ( 91 hom. )

Consequence

CCR2
NM_001123396.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.132

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:

CCR2 (HGNC:):

CCR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 3-46357683-G-T is Benign according to our data. Variant chr3-46357683-G-T is described in ClinVar as [Benign]. Clinvar id is 714233.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.132 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCR2	NM_001123396.4 linkuse as main transcript	c.156G>T	p.Val52Val	synonymous_variant	2/2	ENST00000445132.3	NP_001116868.1	P41597-2A0A024R2Q0
CCR2	NM_001123041.3 linkuse as main transcript	c.156G>T	p.Val52Val	synonymous_variant	2/3		NP_001116513.2	P41597-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CCR2	ENST00000445132.3 linkuse as main transcript	c.156G>T	p.Val52Val	synonymous_variant	2/2	1	NM_001123396.4	ENSP00000399285.2	P41597-2
CCR2	ENST00000400888.2 linkuse as main transcript	c.156G>T	p.Val52Val	synonymous_variant	1/2	1		ENSP00000383681.2	P41597-1
CCR2	ENST00000421659.1 linkuse as main transcript	c.156G>T	p.Val52Val	synonymous_variant	3/3	4		ENSP00000396736.1	E9PH76
CCR2	ENST00000465202.1 linkuse as main transcript	n.315-434G>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00697

AC:

1061

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00171

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00472

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.00643

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00988

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00733

AC:

1843

AN:

251344

Hom.:

AF XY:

0.00785

AC XY:

1067

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00202

Gnomad ASJ exome

AF:

0.00119

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00719

Gnomad FIN exome

AF:

0.0184

Gnomad NFE exome

AF:

0.00935

Gnomad OTH exome

AF:

0.00847

GnomAD4 exome

AF:

0.00903

AC:

13203

AN:

1461876

Hom.:

Cov.:

AF XY:

0.00909

AC XY:

6610

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.00210

Gnomad4 ASJ exome

AF:

0.00107

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00776

Gnomad4 FIN exome

AF:

0.0165

Gnomad4 NFE exome

AF:

0.00993

Gnomad4 OTH exome

AF:

0.00685

GnomAD4 genome

AF:

0.00697

AC:

1061

AN:

152246

Hom.:

Cov.:

AF XY:

0.00767

AC XY:

571

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.00171

Gnomad4 AMR

AF:

0.00471

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.00643

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.00988

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00866

Hom.:

Bravo

AF:

0.00567

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00905

EpiControl

AF:

0.00865

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 31, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

5.7

DANN

Benign

0.62

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over