rs1799987
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NR_125406.1(CCR5AS):n.565+800T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,794 control chromosomes in the GnomAD database, including 18,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 18573 hom., cov: 30)
Consequence
CCR5AS
NR_125406.1 intron, non_coding_transcript
NR_125406.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.587
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 3-46370444-A-G is Benign according to our data. Variant chr3-46370444-A-G is described in ClinVar as [Benign]. Clinvar id is 8189.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR5AS | NR_125406.1 | n.565+800T>C | intron_variant, non_coding_transcript_variant | ||||
CCR5 | NM_000579.4 | c.-301+246A>G | intron_variant | ||||
CCR5 | NM_001100168.2 | c.-66+246A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR5AS | ENST00000701879.1 | n.347+800T>C | intron_variant, non_coding_transcript_variant | ||||||
CCR5AS | ENST00000451485.2 | n.565+800T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.491 AC: 74529AN: 151674Hom.: 18552 Cov.: 30
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.491 AC: 74586AN: 151794Hom.: 18573 Cov.: 30 AF XY: 0.496 AC XY: 36779AN XY: 74166
GnomAD4 genome
?
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36779
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74166
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ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Acquired immunodeficiency syndrome, delayed progression to Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2003 | - - |
CCR5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2021 | 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). - |
Susceptibility to HIV infection Benign:1
protective, no assertion criteria provided | literature only | OMIM | Jul 08, 2003 | - - |
CCR5 PROMOTER POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jul 08, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at