rs708272
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000078.3(CETP):c.118+279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 665,408 control chromosomes in the GnomAD database, including 58,748 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.39 ( 11832 hom., cov: 30)
Exomes 𝑓: 0.42 ( 46916 hom. )
Consequence
CETP
NM_000078.3 intron
NM_000078.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.65
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=-0.98).
BP6
Variant 16-56962376-G-A is Benign according to our data. Variant chr16-56962376-G-A is described in ClinVar as [Benign]. Clinvar id is 1239762.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56962376-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.118+279G>A | intron_variant | ENST00000200676.8 | NP_000069.2 | |||
CETP | NM_001286085.2 | c.118+279G>A | intron_variant | NP_001273014.1 | ||||
CETP | XM_006721124.4 | c.118+279G>A | intron_variant | XP_006721187.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.118+279G>A | intron_variant | 1 | NM_000078.3 | ENSP00000200676 | P1 | |||
CETP | ENST00000379780.6 | c.118+279G>A | intron_variant | 1 | ENSP00000369106 | |||||
CETP | ENST00000566128.1 | c.-78+80G>A | intron_variant | 5 | ENSP00000456276 | |||||
CETP | ENST00000569082.1 | n.116+279G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.385 AC: 58415AN: 151616Hom.: 11821 Cov.: 30
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GnomAD3 exomes AF: 0.424 AC: 96025AN: 226300Hom.: 20571 AF XY: 0.428 AC XY: 53503AN XY: 124984
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GnomAD4 exome AF: 0.423 AC: 217317AN: 513672Hom.: 46916 Cov.: 0 AF XY: 0.427 AC XY: 121515AN XY: 284554
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GnomAD4 genome AF: 0.385 AC: 58469AN: 151736Hom.: 11832 Cov.: 30 AF XY: 0.390 AC XY: 28940AN XY: 74114
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Coronary artery disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Rasad Genetic Department, Rasad Pathobiology and Genetic Laboratory | May 12, 2022 | - - |
Computational scores
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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