rs333
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 4P and 8B. PVS1_StrongBA1
The NM_001394783(CCR5):c.554_585del(p.Ser185IlefsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152034 control chromosomes in the gnomAD Genomes database, including 553 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.072 ( 553 hom., cov: 31)
Exomes 𝑓: 0.074 ( 966 hom. )
Consequence
CCR5
NM_001394783 frameshift
NM_001394783 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.894
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Fraction of 0.48 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR5 | NM_001394783.1 | c.554_585del | p.Ser185IlefsTer32 | frameshift_variant | 2/2 | ENST00000292303.5 | |
CCR5AS | NR_125406.1 | n.392-2067_392-2036del | intron_variant, non_coding_transcript_variant | ||||
CCR5 | NM_000579.4 | c.554_585del | p.Ser185IlefsTer32 | frameshift_variant | 3/3 | ||
CCR5 | NM_001100168.2 | c.554_585del | p.Ser185IlefsTer32 | frameshift_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR5 | ENST00000292303.5 | c.554_585del | p.Ser185IlefsTer32 | frameshift_variant | 2/2 | 1 | NM_001394783.1 | P1 | |
CCR5AS | ENST00000701879.1 | n.174-2067_174-2036del | intron_variant, non_coding_transcript_variant | ||||||
CCR5 | ENST00000445772.1 | c.554_585del | p.Ser185IlefsTer32 | frameshift_variant | 1/1 | P1 | |||
CCR5AS | ENST00000451485.2 | n.392-2067_392-2036del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0718 AC: 10911AN: 152034Hom.: 553 Cov.: 31
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GnomAD3 exomes AF: 0.0743 AC: 18640AN: 251006Hom.: 966 AF XY: 0.0745 AC XY: 10108AN XY: 135678
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ClinVar
Significance: Benign
Submissions summary: Benign:3Other:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2019 | - - |
Susceptibility to HIV infection Benign:1
protective, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
Resistance to hepatitis C virus Benign:1
protective, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
West Nile virus, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
Multiple sclerosis modifier of disease progression Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at