rs715948

chr12-57139199-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 108291 AN: 151858 Hom.: 38962 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.690

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.713 AC: 108389 AN: 151976 Hom.: 39005 Cov.: 31 AF XY: 0.711 AC XY: 52801 AN XY: 74300

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.686

Alfa AF: 0.696 Hom.: 52433

Bravo AF: 0.718

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.7
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs715948; hg19: chr12-57532982;