rs746492
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS2
The NM_001394783.1(CCR5):c.*1860G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000033 in 151,434 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000033 ( 0 hom., cov: 29)
Consequence
CCR5
NM_001394783.1 3_prime_UTR
NM_001394783.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.212
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 Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS2
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCR5 | NM_001394783.1 | c.*1860G>A | 3_prime_UTR_variant | 2/2 | ENST00000292303.5 | NP_001381712.1 | ||
CCR5AS | NR_125406.1 | n.392-4404C>T | intron_variant, non_coding_transcript_variant | |||||
CCR5 | NM_000579.4 | c.*1860G>A | 3_prime_UTR_variant | 3/3 | NP_000570.1 | |||
CCR5 | NM_001100168.2 | c.*1860G>A | 3_prime_UTR_variant | 3/3 | NP_001093638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR5 | ENST00000292303.5 | c.*1860G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_001394783.1 | ENSP00000292303 | P1 | ||
CCR5AS | ENST00000701879.1 | n.174-4404C>T | intron_variant, non_coding_transcript_variant | |||||||
CCR5AS | ENST00000451485.2 | n.392-4404C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151434Hom.: 0 Cov.: 29
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GnomAD4 genome AF: 0.0000330 AC: 5AN: 151434Hom.: 0 Cov.: 29 AF XY: 0.0000270 AC XY: 2AN XY: 73940
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ClinVar
Not reported inComputational scores
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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