19-44907853-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000041.4(APOE):āc.137T>Cā(p.Leu46Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,614,020 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000041.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOE | NM_000041.4 | c.137T>C | p.Leu46Pro | missense_variant | 3/4 | ENST00000252486.9 | NP_000032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOE | ENST00000252486.9 | c.137T>C | p.Leu46Pro | missense_variant | 3/4 | 1 | NM_000041.4 | ENSP00000252486.3 | ||
APOE | ENST00000425718.1 | c.137T>C | p.Leu46Pro | missense_variant | 2/3 | 1 | ENSP00000410423.1 | |||
APOE | ENST00000434152.5 | c.215T>C | p.Leu72Pro | missense_variant | 3/4 | 2 | ENSP00000413653.2 | |||
APOE | ENST00000446996.5 | c.137T>C | p.Leu46Pro | missense_variant | 3/4 | 2 | ENSP00000413135.1 |
Frequencies
GnomAD3 genomes AF: 0.00193 AC: 293AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00251 AC: 629AN: 250698Hom.: 4 AF XY: 0.00243 AC XY: 329AN XY: 135650
GnomAD4 exome AF: 0.00203 AC: 2961AN: 1461714Hom.: 6 Cov.: 32 AF XY: 0.00200 AC XY: 1451AN XY: 727148
GnomAD4 genome AF: 0.00192 AC: 293AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74480
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 19, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | May 12, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2020 | This variant is associated with the following publications: (PMID: 24126160, 24082139, 11068149, 22530123, 10213152, 23990795, 26802169, 16621646, 26206375, 24644280) - |
Alzheimer disease 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2016 | This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PS3. - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 08, 2020 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at