chr19-44907806-C-G
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000041.4(APOE):āc.90C>Gā(p.Pro30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,613,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00015 ( 0 hom., cov: 32)
Exomes š: 0.00030 ( 0 hom. )
Consequence
APOE
NM_000041.4 synonymous
NM_000041.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.47
Genes affected
APOE (HGNC:613): (apolipoprotein E) The protein encoded by this gene is a major apoprotein of the chylomicron. It binds to a specific liver and peripheral cell receptor, and is essential for the normal catabolism of triglyceride-rich lipoprotein constituents. This gene maps to chromosome 19 in a cluster with the related apolipoprotein C1 and C2 genes. Mutations in this gene result in familial dysbetalipoproteinemia, or type III hyperlipoproteinemia (HLP III), in which increased plasma cholesterol and triglycerides are the consequence of impaired clearance of chylomicron and VLDL remnants. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 19-44907806-C-G is Benign according to our data. Variant chr19-44907806-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1209987.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-44907806-C-G is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-2.47 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOE | NM_000041.4 | c.90C>G | p.Pro30= | synonymous_variant | 3/4 | ENST00000252486.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOE | ENST00000252486.9 | c.90C>G | p.Pro30= | synonymous_variant | 3/4 | 1 | NM_000041.4 | P1 | |
APOE | ENST00000425718.1 | c.90C>G | p.Pro30= | synonymous_variant | 2/3 | 1 | |||
APOE | ENST00000434152.5 | c.168C>G | p.Pro56= | synonymous_variant | 3/4 | 2 | |||
APOE | ENST00000446996.5 | c.90C>G | p.Pro30= | synonymous_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152156Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000116 AC: 29AN: 249392Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135124
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GnomAD4 exome AF: 0.000304 AC: 445AN: 1461446Hom.: 0 Cov.: 32 AF XY: 0.000290 AC XY: 211AN XY: 727030
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74342
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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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