rs1800941
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_001394783.1(CCR5):āc.225T>Cā(p.Ser75Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000303 in 1,614,052 control chromosomes in the GnomAD database, including 1 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: š 0.0018 ( 1 hom., cov: 32)
Exomes š: 0.00015 ( 0 hom. )
Consequence
CCR5
NM_001394783.1 synonymous
NM_001394783.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.83
Genes affected
CCR5 (HGNC:1606): (C-C motif chemokine receptor 5) This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. This protein is expressed by T cells and macrophages, and is known to be an important co-receptor for macrophage-tropic virus, including HIV, to enter host cells. Defective alleles of this gene have been associated with the HIV infection resistance. The ligands of this receptor include monocyte chemoattractant protein 2 (MCP-2), macrophage inflammatory protein 1 alpha (MIP-1 alpha), macrophage inflammatory protein 1 beta (MIP-1 beta) and regulated on activation normal T expressed and secreted protein (RANTES). Expression of this gene was also detected in a promyeloblastic cell line, suggesting that this protein may play a role in granulocyte lineage proliferation and differentiation. This gene is located at the chemokine receptor gene cluster region. An allelic polymorphism in this gene results in both functional and non-functional alleles; the reference genome represents the functional allele. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
Synonymous conserved (PhyloP=-2.84 with no splicing effect.
BS2
High AC in GnomAd4 at 267 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCR5 | NM_001394783.1 | c.225T>C | p.Ser75Ser | synonymous_variant | 2/2 | ENST00000292303.5 | NP_001381712.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR5 | ENST00000292303.5 | c.225T>C | p.Ser75Ser | synonymous_variant | 2/2 | 1 | NM_001394783.1 | ENSP00000292303.4 | ||
CCR5 | ENST00000445772.1 | c.225T>C | p.Ser75Ser | synonymous_variant | 1/1 | 6 | ENSP00000404881.1 | |||
CCR5AS | ENST00000451485.2 | n.392-1710A>G | intron_variant | 3 | ||||||
CCR5AS | ENST00000701879.1 | n.174-1710A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00175 AC: 267AN: 152212Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000477 AC: 120AN: 251324Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135816
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GnomAD4 exome AF: 0.000152 AC: 222AN: 1461722Hom.: 0 Cov.: 32 AF XY: 0.000127 AC XY: 92AN XY: 727186
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GnomAD4 genome AF: 0.00175 AC: 267AN: 152330Hom.: 1 Cov.: 32 AF XY: 0.00160 AC XY: 119AN XY: 74498
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Not reported inComputational 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