rs3820198
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004631.5(LRP8):āc.138T>Gā(p.Asp46Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,613,024 control chromosomes in the GnomAD database, including 129,517 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004631.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP8 | NM_004631.5 | c.138T>G | p.Asp46Glu | missense_variant | 2/19 | ENST00000306052.12 | |
LRP8 | NM_001018054.3 | c.138T>G | p.Asp46Glu | missense_variant | 2/18 | ||
LRP8 | NM_033300.4 | c.138T>G | p.Asp46Glu | missense_variant | 2/17 | ||
LRP8 | NM_017522.5 | c.138T>G | p.Asp46Glu | missense_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP8 | ENST00000306052.12 | c.138T>G | p.Asp46Glu | missense_variant | 2/19 | 1 | NM_004631.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.497 AC: 75507AN: 152008Hom.: 22380 Cov.: 33
GnomAD3 exomes AF: 0.396 AC: 99269AN: 250518Hom.: 22064 AF XY: 0.395 AC XY: 53506AN XY: 135550
GnomAD4 exome AF: 0.373 AC: 544810AN: 1460898Hom.: 107081 Cov.: 48 AF XY: 0.374 AC XY: 272137AN XY: 726826
GnomAD4 genome ? AF: 0.497 AC: 75611AN: 152126Hom.: 22436 Cov.: 33 AF XY: 0.495 AC XY: 36811AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at