rs41512547
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001394783.1(CCR5):c.*1779C>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 0.00869 in 152,052 control chromosomes in the GnomAD database, including 27 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 0.0087 ( 27 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CCR5
NM_001394783.1 3_prime_UTR
NM_001394783.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.117
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00869 (1322/152052) while in subpopulation AFR AF= 0.0301 (1247/41490). AF 95% confidence interval is 0.0287. There are 27 homozygotes in gnomad4. There are 622 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1322 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR5 | NM_001394783.1 | c.*1779C>G | 3_prime_UTR_variant | 2/2 | ENST00000292303.5 | ||
CCR5AS | NR_125406.1 | n.392-4323G>C | intron_variant, non_coding_transcript_variant | ||||
CCR5 | NM_000579.4 | c.*1779C>G | 3_prime_UTR_variant | 3/3 | |||
CCR5 | NM_001100168.2 | c.*1779C>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR5 | ENST00000292303.5 | c.*1779C>G | 3_prime_UTR_variant | 2/2 | 1 | NM_001394783.1 | P1 | ||
CCR5AS | ENST00000701879.1 | n.174-4323G>C | intron_variant, non_coding_transcript_variant | ||||||
CCR5AS | ENST00000451485.2 | n.392-4323G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00864 AC: 1312AN: 151934Hom.: 27 Cov.: 30
GnomAD3 genomes
AF:
AC:
1312
AN:
151934
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 14886Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 7074
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
14886
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
7074
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00869 AC: 1322AN: 152052Hom.: 27 Cov.: 30 AF XY: 0.00837 AC XY: 622AN XY: 74332
GnomAD4 genome
AF:
AC:
1322
AN:
152052
Hom.:
Cov.:
30
AF XY:
AC XY:
622
AN XY:
74332
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at