chr19-44907807-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000041.4(APOE):c.91G>A(p.Glu31Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000041.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOE | NM_000041.4 | c.91G>A | p.Glu31Lys | missense_variant | 3/4 | ENST00000252486.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOE | ENST00000252486.9 | c.91G>A | p.Glu31Lys | missense_variant | 3/4 | 1 | NM_000041.4 | P1 | |
APOE | ENST00000425718.1 | c.91G>A | p.Glu31Lys | missense_variant | 2/3 | 1 | |||
APOE | ENST00000434152.5 | c.169G>A | p.Glu57Lys | missense_variant | 3/4 | 2 | |||
APOE | ENST00000446996.5 | c.91G>A | p.Glu31Lys | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249636Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135246
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461496Hom.: 0 Cov.: 32 AF XY: 0.0000536 AC XY: 39AN XY: 727060
GnomAD4 genome ? AF: 0.000473 AC: 72AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74474
ClinVar
Submissions by phenotype
APOE5 VARIANT Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 1991 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2019 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at