rs5742907
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 16P and 1B. PVS1PP5_Very_StrongBS1_Supporting
The NM_000078.3(CETP):c.1321+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,614,016 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000078.3 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CETP | NM_000078.3 | c.1321+1G>A | splice_donor_variant, intron_variant | ENST00000200676.8 | NP_000069.2 | |||
CETP | NM_001286085.2 | c.1141+1G>A | splice_donor_variant, intron_variant | NP_001273014.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CETP | ENST00000200676.8 | c.1321+1G>A | splice_donor_variant, intron_variant | 1 | NM_000078.3 | ENSP00000200676.3 | ||||
CETP | ENST00000379780.6 | c.1141+1G>A | splice_donor_variant, intron_variant | 1 | ENSP00000369106.2 | |||||
CETP | ENST00000566128.1 | c.1126+1G>A | splice_donor_variant, intron_variant | 5 | ENSP00000456276.1 | |||||
CETP | ENST00000650358.1 | n.1719+1G>A | splice_donor_variant, intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251424Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135888
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461770Hom.: 1 Cov.: 34 AF XY: 0.000100 AC XY: 73AN XY: 727204
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74450
ClinVar
Submissions by phenotype
Hyperalphalipoproteinemia 1 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 30, 2023 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 1990 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Dec 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at