rs289742
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The 16-56983850-C-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 658,144 control chromosomes in the GnomAD database, including 232,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.80 ( 49781 hom., cov: 31)
Exomes 𝑓: 0.85 ( 183008 hom. )
Consequence
CETP
NM_000078.3 downstream_gene
NM_000078.3 downstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.177
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 16-56983850-C-G is Benign according to our data. Variant chr16-56983850-C-G is described in ClinVar as [Benign]. Clinvar id is 369116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.
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: 0.802 AC: 121907AN: 151946Hom.: 49744 Cov.: 31
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GnomAD4 exome AF: 0.848 AC: 429404AN: 506080Hom.: 183008 Cov.: 5 AF XY: 0.847 AC XY: 231377AN XY: 273056
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GnomAD4 genome ? AF: 0.802 AC: 121998AN: 152064Hom.: 49781 Cov.: 31 AF XY: 0.800 AC XY: 59465AN XY: 74350
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Hyperalphalipoproteinemia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at