11-116830508-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000040.3(APOC3):c.-13-62C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00359 in 1,589,308 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 101 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 83 hom. )
Consequence
APOC3
NM_000040.3 intron
NM_000040.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.772
Genes affected
APOC3 (HGNC:610): (apolipoprotein C3) This gene encodes a protein component of triglyceride (TG)-rich lipoproteins (TRLs) including very low density lipoproteins (VLDL), high density lipoproteins (HDL) and chylomicrons. The encoded protein plays a role in role in the metabolism of these TRLs through multiple modes. This protein has been shown to promote the secretion of VLDL1, inhibit lipoprotein lipase enzyme activity, and delay catabolism of TRL remnants. Mutations in this gene are associated with low plasma triglyceride levels and reduced risk of ischemic cardiovascular disease, and hyperalphalipoproteinemia, which is characterized by elevated levels of high density lipoprotein (HDL) and HDL cholesterol in human patients. This gene and other related genes comprise an apolipoprotein gene cluster on chromosome 11. [provided by RefSeq, Sep 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 11-116830508-C-T is Benign according to our data. Variant chr11-116830508-C-T is described in ClinVar as [Benign]. Clinvar id is 1287928.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0615 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOC3 | NM_000040.3 | c.-13-62C>T | intron_variant | ENST00000227667.8 | NP_000031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOC3 | ENST00000227667.8 | c.-13-62C>T | intron_variant | 1 | NM_000040.3 | ENSP00000227667 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0183 AC: 2777AN: 152158Hom.: 98 Cov.: 32
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GnomAD3 exomes AF: 0.00460 AC: 1100AN: 239090Hom.: 42 AF XY: 0.00351 AC XY: 455AN XY: 129510
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GnomAD4 exome AF: 0.00202 AC: 2907AN: 1437032Hom.: 83 Cov.: 29 AF XY: 0.00178 AC XY: 1274AN XY: 715714
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GnomAD4 genome AF: 0.0184 AC: 2800AN: 152276Hom.: 101 Cov.: 32 AF XY: 0.0179 AC XY: 1334AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 21, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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