16-56983884-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The 16-56983884-G-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 579,590 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 0.000020 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000026 ( 0 hom. )
Consequence
CETP
NM_000078.3 downstream_gene
NM_000078.3 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.72
Genes affected
CETP (HGNC:1869): (cholesteryl ester transfer protein) The protein encoded by this gene is found in plasma, where it is involved in the transfer of cholesteryl ester from high density lipoprotein (HDL) to other lipoproteins. Defects in this gene are a cause of hyperalphalipoproteinemia 1 (HALP1). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | downstream_gene_variant | ENST00000200676.8 | ||||
CETP | NM_001286085.2 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | downstream_gene_variant | 1 | NM_000078.3 | P1 | ||||
CETP | ENST00000379780.6 | downstream_gene_variant | 1 | ||||||
CETP | ENST00000566128.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151884Hom.: 0 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.0000257 AC: 11AN: 427706Hom.: 0 Cov.: 3 AF XY: 0.0000261 AC XY: 6AN XY: 230102
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151884Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74166
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at