rs3138042
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001123396.4(CCR2):c.*931A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,043,916 control chromosomes in the GnomAD database, including 51,376 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 0.32 ( 7817 hom., cov: 32)
Exomes 𝑓: 0.31 ( 43559 hom. )
Consequence
CCR2
NM_001123396.4 3_prime_UTR
NM_001123396.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.51
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
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 | UniProt |
---|---|---|---|---|---|---|---|
CCR2 | NM_001123396.4 | c.*931A>G | 3_prime_UTR_variant | 2/2 | ENST00000445132.3 | ||
CCR2 | NM_001123041.3 | c.942-136A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR2 | ENST00000445132.3 | c.*931A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_001123396.4 | P2 | ||
CCR2 | ENST00000400888.2 | c.942-136A>G | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.320 AC: 48561AN: 151798Hom.: 7800 Cov.: 32
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GnomAD4 exome AF: 0.309 AC: 275829AN: 892002Hom.: 43559 Cov.: 12 AF XY: 0.311 AC XY: 138647AN XY: 445868
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GnomAD4 genome ? AF: 0.320 AC: 48596AN: 151914Hom.: 7817 Cov.: 32 AF XY: 0.322 AC XY: 23921AN XY: 74248
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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