chr3-46358376-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001123396.4(CCR2):c.849G>T(p.Leu283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000929 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00031 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000070 ( 0 hom. )
Consequence
CCR2
NM_001123396.4 synonymous
NM_001123396.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.621
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
Variant 3-46358376-G-T is Benign according to our data. Variant chr3-46358376-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3052543.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.621 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR2 | NM_001123396.4 | c.849G>T | p.Leu283= | synonymous_variant | 2/2 | ENST00000445132.3 | |
CCR2 | NM_001123041.3 | c.849G>T | p.Leu283= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR2 | ENST00000445132.3 | c.849G>T | p.Leu283= | synonymous_variant | 2/2 | 1 | NM_001123396.4 | P2 | |
CCR2 | ENST00000400888.2 | c.849G>T | p.Leu283= | synonymous_variant | 1/2 | 1 | A2 | ||
CCR2 | ENST00000465202.1 | n.574G>T | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152098Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000104 AC: 26AN: 250766Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135694
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GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461868Hom.: 0 Cov.: 34 AF XY: 0.0000591 AC XY: 43AN XY: 727242
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GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74428
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CCR2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at