rs12721052
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000592535.6(APOC1):c.195-457del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 157,762 control chromosomes in the GnomAD database, including 7,439 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 7156 hom., cov: 0)
Exomes 𝑓: 0.26 ( 283 hom. )
Consequence
APOC1
ENST00000592535.6 intron
ENST00000592535.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.293
Genes affected
APOC1 (HGNC:607): (apolipoprotein C1) This gene encodes a member of the apolipoprotein C1 family. This gene is expressed primarily in the liver, and it is activated when monocytes differentiate into macrophages. The encoded protein plays a central role in high density lipoprotein (HDL) and very low density lipoprotein (VLDL) metabolism. This protein has also been shown to inhibit cholesteryl ester transfer protein in plasma. A pseudogene of this gene is located 4 kb downstream in the same orientation, on the same chromosome. This gene is mapped to chromosome 19, where it resides within a apolipoprotein gene cluster. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOC1 | NM_001645.5 | c.195-457del | intron_variant | ENST00000592535.6 | NP_001636.1 | |||
APOC1 | NM_001321065.2 | c.195-457del | intron_variant | NP_001307994.1 | ||||
APOC1 | NM_001321066.2 | c.195-457del | intron_variant | NP_001307995.1 | ||||
APOC1 | NM_001379687.1 | c.340-457del | intron_variant | NP_001366616.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOC1 | ENST00000592535.6 | c.195-457del | intron_variant | 1 | NM_001645.5 | ENSP00000468276 | P1 |
Frequencies
GnomAD3 genomes AF: 0.307 AC: 46244AN: 150710Hom.: 7157 Cov.: 0
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GnomAD4 exome AF: 0.260 AC: 1800AN: 6934Hom.: 283 AF XY: 0.262 AC XY: 953AN XY: 3632
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GnomAD4 genome AF: 0.307 AC: 46259AN: 150828Hom.: 7156 Cov.: 0 AF XY: 0.306 AC XY: 22495AN XY: 73630
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at