17-34256250-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002982.4(CCL2):āc.105T>Cā(p.Cys35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,609,614 control chromosomes in the GnomAD database, including 133,317 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.47 ( 18471 hom., cov: 32)
Exomes š: 0.39 ( 114846 hom. )
Consequence
CCL2
NM_002982.4 synonymous
NM_002982.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.394
Genes affected
CCL2 (HGNC:10618): (C-C motif chemokine ligand 2) This gene is one of several cytokine genes clustered on the q-arm of chromosome 17. Chemokines are a superfamily of secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of N-terminal cysteine residues of the mature peptide. This chemokine is a member of the CC subfamily which is characterized by two adjacent cysteine residues. This cytokine displays chemotactic activity for monocytes and basophils but not for neutrophils or eosinophils. It has been implicated in the pathogenesis of diseases characterized by monocytic infiltrates, like psoriasis, rheumatoid arthritis and atherosclerosis. It binds to chemokine receptors CCR2 and CCR4. Elevated expression of the encoded protein is associated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. [provided by RefSeq, Aug 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 17-34256250-T-C is Benign according to our data. Variant chr17-34256250-T-C is described in ClinVar as [Benign]. Clinvar id is 3059105.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=0.394 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL2 | NM_002982.4 | c.105T>C | p.Cys35= | synonymous_variant | 2/3 | ENST00000225831.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL2 | ENST00000225831.4 | c.105T>C | p.Cys35= | synonymous_variant | 2/3 | 1 | NM_002982.4 | P1 | |
CCL2 | ENST00000580907.6 | c.105T>C | p.Cys35= | synonymous_variant | 2/2 | 2 | |||
CCL2 | ENST00000624362.2 | n.966T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.474 AC: 72025AN: 151884Hom.: 18430 Cov.: 32
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GnomAD3 exomes AF: 0.444 AC: 111431AN: 250930Hom.: 26499 AF XY: 0.431 AC XY: 58446AN XY: 135582
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GnomAD4 exome AF: 0.388 AC: 565637AN: 1457608Hom.: 114846 Cov.: 31 AF XY: 0.388 AC XY: 281380AN XY: 725212
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GnomAD4 genome ? AF: 0.474 AC: 72121AN: 152006Hom.: 18471 Cov.: 32 AF XY: 0.478 AC XY: 35499AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CCL2-related disorder Benign:1
Benign, criteria provided, single submitter | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at