chr3-46370768-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_125406.1(CCR5AS):n.565+476G>A 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 0.492 in 151,988 control chromosomes in the GnomAD database, including 18,629 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 0.49 ( 18629 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
CCR5AS
NR_125406.1 intron, non_coding_transcript
NR_125406.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.769
Genes affected
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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).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR5AS | NR_125406.1 | n.565+476G>A | intron_variant, non_coding_transcript_variant | ||||
CCR5 | NM_000579.4 | c.-232C>T | 5_prime_UTR_variant | 2/3 | |||
CCR5 | NM_001100168.2 | c.-65-167C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR5AS | ENST00000701879.1 | n.347+476G>A | intron_variant, non_coding_transcript_variant | ||||||
CCR5AS | ENST00000451485.2 | n.565+476G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.492 AC: 74711AN: 151870Hom.: 18608 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.492 AC: 74767AN: 151988Hom.: 18629 Cov.: 32 AF XY: 0.497 AC XY: 36897AN XY: 74282
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at