rs715948
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002332.3(LRP1):c.190+618T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,976 control chromosomes in the GnomAD database, including 39,005 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.71 ( 39005 hom., cov: 31)
Consequence
LRP1
NM_002332.3 intron
NM_002332.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.413
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRP1 | NM_002332.3 | c.190+618T>C | intron_variant | ENST00000243077.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRP1 | ENST00000243077.8 | c.190+618T>C | intron_variant | 1 | NM_002332.3 | P1 | |||
LRP1 | ENST00000338962.8 | c.190+618T>C | intron_variant | 1 | |||||
LRP1 | ENST00000553277.5 | c.190+618T>C | intron_variant | 1 | |||||
LRP1 | ENST00000554174.1 | c.190+618T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.713 AC: 108291AN: 151858Hom.: 38962 Cov.: 31
GnomAD3 genomes
?
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108291
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.713 AC: 108389AN: 151976Hom.: 39005 Cov.: 31 AF XY: 0.711 AC XY: 52801AN XY: 74300
GnomAD4 genome
?
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108389
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151976
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31
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52801
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74300
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2269
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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