Variant 3-46358307-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001123396.4(CCR2):c.780T>C(p.Asn260Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,613,876 control chromosomes in the GnomAD database, including 80,922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.32 ( 7841 hom., cov: 32)

Exomes 𝑓: 0.31 ( 73081 hom. )

Consequence

CCR2
NM_001123396.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.70

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 3-46358307-T-C is Benign according to our data. Variant chr3-46358307-T-C is described in ClinVar as [Benign]. Clinvar id is 3059948.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.7 with no splicing effect.

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/exons	MANE	Protein	UniProt
CCR2	NM_001123396.4 linkuse as main transcript	c.780T>C	p.Asn260Asn	synonymous_variant	2/2	ENST00000445132.3	NP_001116868.1	P41597-2A0A024R2Q0
CCR2	NM_001123041.3 linkuse as main transcript	c.780T>C	p.Asn260Asn	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.780T>C	p.Asn260Asn	synonymous_variant	2/2	1	NM_001123396.4	ENSP00000399285.2	P41597-2
CCR2	ENST00000400888.2 linkuse as main transcript	c.780T>C	p.Asn260Asn	synonymous_variant	1/2	1		ENSP00000383681.2	P41597-1
CCR2	ENST00000465202.1 linkuse as main transcript	n.505T>C		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48628

AN:

151928

Hom.:

7823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.301

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

GnomAD3 exomes

AF:

0.320

AC:

80079

AN:

250390

Hom.:

13119

AF XY:

0.323

AC XY:

43790

AN XY:

135670

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.263

Gnomad EAS exome

AF:

0.328

Gnomad SAS exome

AF:

0.363

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.314

AC:

459207

AN:

1461830

Hom.:

73081

Cov.:

AF XY:

0.316

AC XY:

229821

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.322

GnomAD4 genome

AF:

0.320

AC:

48665

AN:

152046

Hom.:

7841

Cov.:

AF XY:

0.322

AC XY:

23956

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.332

Gnomad4 AMR

AF:

0.354

Gnomad4 ASJ

AF:

0.269

Gnomad4 EAS

AF:

0.312

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.310

Gnomad4 OTH

AF:

0.334

Alfa

AF:

0.310

Hom.:

3368

Bravo

AF:

0.323

Asia WGS

AF:

0.307

AC:

1066

AN:

3478

EpiCase

AF:

0.332

EpiControl

AF:

0.324

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CCR2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.2

DANN

Benign

0.30

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