rs1466535

chr12-57140687-G-Achr12-57140687-G-C

Variant summary

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

The NM_002332.3(LRP1):c.191-687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,014 control chromosomes in the GnomAD database, including 7,445 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 0.30 (7445 hom., cov: 31)
• Consequence: LRP1 NM_002332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP1	NM_002332.3	c.191-687G>A		intron_variant		ENST00000243077.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP1	ENST00000243077.8	c.191-687G>A		intron_variant		1	NM_002332.3	P1
LRP1	ENST00000338962.8	c.191-687G>A		intron_variant		1
LRP1	ENST00000553277.5	c.191-687G>A		intron_variant		1
LRP1	ENST00000554174.1	c.191-687G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45960 AN: 151896 Hom.: 7440 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.302 AC: 45980 AN: 152014 Hom.: 7445 Cov.: 31 AF XY: 0.303 AC XY: 22521 AN XY: 74304

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.285

Alfa AF: 0.332 Hom.: 11678

Bravo AF: 0.305

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.2
Dann	Benign	0.72

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: rs1466535; hg19: chr12-57534470;