rs3092964

Variant names:

• chr3-46354094-G-A
• rs3092964
• ENST00000465202.1:n.231G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-46354094-G-A
• chr3-46354094-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCR2	NM_001123396.4	c.-135G>A		upstream_gene_variant		ENST00000445132.3	NP_001116868.1
CCR2	NM_001123041.3	c.-135G>A		upstream_gene_variant			NP_001116513.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCR2	ENST00000465202.1	n.231G>A		non_coding_transcript_exon_variant	Exon 1 of 2	5
CCR2	ENST00000445132.3	c.-135G>A		upstream_gene_variant		1	NM_001123396.4	ENSP00000399285.2
CCR2	ENST00000421659.1	c.-230G>A		upstream_gene_variant		4		ENSP00000396736.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.896 AC: 37160 AN: 41466

American (AMR) AF: 0.708 AC: 10813 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2740 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3738 AN: 5174

South Asian (SAS) AF: 0.843 AC: 4063 AN: 4818

European-Finnish (FIN) AF: 0.848 AC: 8934 AN: 10536

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.759 AC: 51613 AN: 67988

Other (OTH) AF: 0.766 AC: 1613 AN: 2106

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
PhyloP100		-0.27
PromoterAI		0.0082	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3092964; hg19: chr3-46395585;