rs11172124
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002332.3(LRP1):c.10345+19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,612,808 control chromosomes in the GnomAD database, including 47,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.22 ( 3811 hom., cov: 31)
Exomes 𝑓: 0.24 ( 43498 hom. )
Consequence
LRP1
NM_002332.3 intron
NM_002332.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.03
Genes affected
LRP1 (HGNC:6692): (LDL receptor related protein 1) This gene encodes a member of the low-density lipoprotein receptor family of proteins. The encoded preproprotein is proteolytically processed by furin to generate 515 kDa and 85 kDa subunits that form the mature receptor (PMID: 8546712). This receptor is involved in several cellular processes, including intracellular signaling, lipid homeostasis, and clearance of apoptotic cells. In addition, the encoded protein is necessary for the alpha 2-macroglobulin-mediated clearance of secreted amyloid precursor protein and beta-amyloid, the main component of amyloid plaques found in Alzheimer patients. Expression of this gene decreases with age and has been found to be lower than controls in brain tissue from Alzheimer's disease patients. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 12-57201172-G-A is Benign according to our data. Variant chr12-57201172-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP1 | ENST00000243077.8 | c.10345+19G>A | intron_variant | 1 | NM_002332.3 | ENSP00000243077.3 | ||||
LRP1 | ENST00000555124.1 | c.46+19G>A | intron_variant | 4 | ENSP00000451012.1 | |||||
LRP1 | ENST00000555941.1 | n.*19G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.218 AC: 33173AN: 152002Hom.: 3810 Cov.: 31
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GnomAD3 exomes AF: 0.225 AC: 56331AN: 250486Hom.: 6935 AF XY: 0.218 AC XY: 29474AN XY: 135358
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GnomAD4 exome AF: 0.239 AC: 348636AN: 1460688Hom.: 43498 Cov.: 37 AF XY: 0.234 AC XY: 170107AN XY: 726440
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GnomAD4 genome AF: 0.218 AC: 33188AN: 152120Hom.: 3811 Cov.: 31 AF XY: 0.214 AC XY: 15947AN XY: 74358
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ClinVar
Not reported inComputational 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at