rs291044
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000078.3(CETP):c.982-551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,016 control chromosomes in the GnomAD database, including 6,831 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.28 ( 6831 hom., cov: 32)
Consequence
CETP
NM_000078.3 intron
NM_000078.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.747
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.982-551G>A | intron_variant | Intron 10 of 15 | ENST00000200676.8 | NP_000069.2 | ||
CETP | NM_001286085.2 | c.802-551G>A | intron_variant | Intron 9 of 14 | NP_001273014.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.982-551G>A | intron_variant | Intron 10 of 15 | 1 | NM_000078.3 | ENSP00000200676.3 | |||
CETP | ENST00000379780.6 | c.802-551G>A | intron_variant | Intron 9 of 14 | 1 | ENSP00000369106.2 | ||||
CETP | ENST00000566128.1 | c.787-551G>A | intron_variant | Intron 10 of 15 | 5 | ENSP00000456276.1 | ||||
CETP | ENST00000650358.1 | n.829G>A | non_coding_transcript_exon_variant | Exon 1 of 5 |
Frequencies
GnomAD3 genomes AF: 0.285 AC: 43282AN: 151898Hom.: 6830 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.285 AC: 43292AN: 152016Hom.: 6831 Cov.: 32 AF XY: 0.285 AC XY: 21153AN XY: 74302
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1109
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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