rs3092964

chr3-46354094-G-Achr3-46354094-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465202.1(CCR2):n.231G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,022 control chromosomes in the GnomAD database, including 49,043 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 0.80 (49042 hom., cov: 30)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CCR2 ENST00000465202.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCR2	NM_001123396.4			upstream_gene_variant		ENST00000445132.3
CCR2	NM_001123041.3			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCR2	ENST00000465202.1	n.231G>A		non_coding_transcript_exon_variant	1/2	5
CCR2	ENST00000445132.3			upstream_gene_variant		1	NM_001123396.4	P2
CCR2	ENST00000421659.1			upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121522 AN: 151902 Hom.: 48981 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.764

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.800 AC: 121638 AN: 152020 Hom.: 49042 Cov.: 30 AF XY: 0.801 AC XY: 59539 AN XY: 74292

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.766

Alfa AF: 0.785 Hom.: 9177

Bravo AF: 0.794

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	3.0
Dann	Benign	0.58

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

Other links and lift over

dbSNP: rs3092964; hg19: chr3-46395585;