rs711752
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000078.3(CETP):c.118+202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 737,362 control chromosomes in the GnomAD database, including 65,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 11865 hom., cov: 31)
Exomes 𝑓: 0.42 ( 53322 hom. )
Consequence
CETP
NM_000078.3 intron
NM_000078.3 intron
Scores
2
Splicing: ADA: 0.0001408
2
Clinical Significance
Conservation
PhyloP100: 1.01
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=-0.82).
BP6
?
Variant 16-56962299-G-A is Benign according to our data. Variant chr16-56962299-G-A is described in ClinVar as [Benign]. Clinvar id is 1255212.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-56962299-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.118+202G>A | intron_variant | ENST00000200676.8 | |||
CETP | NM_001286085.2 | c.118+202G>A | intron_variant | ||||
CETP | XM_006721124.4 | c.118+202G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.118+202G>A | intron_variant | 1 | NM_000078.3 | P1 | |||
CETP | ENST00000379780.6 | c.118+202G>A | intron_variant | 1 | |||||
CETP | ENST00000566128.1 | c.-78+3G>A | splice_donor_region_variant, intron_variant | 5 | |||||
CETP | ENST00000569082.1 | n.116+202G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.386 AC: 58532AN: 151832Hom.: 11855 Cov.: 31
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GnomAD4 exome AF: 0.424 AC: 248464AN: 585410Hom.: 53322 Cov.: 3 AF XY: 0.428 AC XY: 136870AN XY: 319762
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GnomAD4 genome ? AF: 0.386 AC: 58585AN: 151952Hom.: 11865 Cov.: 31 AF XY: 0.391 AC XY: 29016AN XY: 74246
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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 | Aug 30, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at