rs1532624
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000200676.8(CETP):c.658+186C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,090 control chromosomes in the GnomAD database, including 10,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.34 ( 10327 hom., cov: 33)
Consequence
CETP
ENST00000200676.8 intron
ENST00000200676.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0590
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 16-56971567-C-A is Benign according to our data. Variant chr16-56971567-C-A is described in ClinVar as [Benign]. Clinvar id is 225955.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-56971567-C-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.658+186C>A | intron_variant | ENST00000200676.8 | NP_000069.2 | |||
CETP | NM_001286085.2 | c.658+186C>A | intron_variant | NP_001273014.1 | ||||
CETP | XM_006721124.4 | c.658+186C>A | intron_variant | XP_006721187.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.658+186C>A | intron_variant | 1 | NM_000078.3 | ENSP00000200676 | P1 | |||
CETP | ENST00000379780.6 | c.658+186C>A | intron_variant | 1 | ENSP00000369106 | |||||
CETP | ENST00000566128.1 | c.463+186C>A | intron_variant | 5 | ENSP00000456276 | |||||
CETP | ENST00000569082.1 | n.760+186C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.344 AC: 52339AN: 151970Hom.: 10332 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.344 AC: 52329AN: 152090Hom.: 10327 Cov.: 33 AF XY: 0.346 AC XY: 25749AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2019 | - - |
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