rs1801706
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000078.3(CETP):c.*84G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,303,282 control chromosomes in the GnomAD database, including 20,279 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2198 hom., cov: 32)
Exomes 𝑓: 0.17 ( 18081 hom. )
Consequence
CETP
NM_000078.3 3_prime_UTR
NM_000078.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.20
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=-0.9).
BP6
?
Variant 16-56983750-G-A is Benign according to our data. Variant chr16-56983750-G-A is described in ClinVar as [Benign]. Clinvar id is 320000.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56983750-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.*84G>A | 3_prime_UTR_variant | 16/16 | ENST00000200676.8 | ||
CETP | NM_001286085.2 | c.*84G>A | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.*84G>A | 3_prime_UTR_variant | 16/16 | 1 | NM_000078.3 | P1 | ||
CETP | ENST00000379780.6 | c.*84G>A | 3_prime_UTR_variant | 15/15 | 1 | ||||
CETP | ENST00000566128.1 | c.*84G>A | 3_prime_UTR_variant | 16/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.165 AC: 25083AN: 152024Hom.: 2198 Cov.: 32
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GnomAD4 exome AF: 0.174 AC: 199929AN: 1151140Hom.: 18081 Cov.: 16 AF XY: 0.175 AC XY: 102613AN XY: 587044
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GnomAD4 genome ? AF: 0.165 AC: 25095AN: 152142Hom.: 2198 Cov.: 32 AF XY: 0.164 AC XY: 12174AN XY: 74362
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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 | Sep 17, 2018 | This variant is associated with the following publications: (PMID: 8830936, 27768712) - |
Hyperalphalipoproteinemia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at