rs4667593

chr2-169151876-G-A

Variant summary

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

The NM_004525.3(LRP2):c.12462-850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,898 control chromosomes in the GnomAD database, including 16,838 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 0.46 (16838 hom., cov: 31)
• Consequence: LRP2 NM_004525.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

LRP2 (HGNC:6694): (LDL receptor related protein 2) The protein encoded by this gene, low density lipoprotein-related protein 2 (LRP2) or megalin, is a multi-ligand endocytic receptor that is expressed in many different tissues but primarily in absorptive epithilial tissues such as the kidney. This glycoprotein has a large amino-terminal extracellular domain, a single transmembrane domain, and a short carboxy-terminal cytoplasmic tail. The extracellular ligand-binding-domains bind diverse macromolecules including albumin, apolipoproteins B and E, and lipoprotein lipase. The LRP2 protein is critical for the reuptake of numerous ligands, including lipoproteins, sterols, vitamin-binding proteins, and hormones. This protein also has a role in cell-signaling; extracellular ligands include parathyroid horomones and the morphogen sonic hedgehog while cytosolic ligands include MAP kinase scaffold proteins and JNK interacting proteins. Recycling of this membrane receptor is regulated by phosphorylation of its cytoplasmic domain. Mutations in this gene cause Donnai-Barrow syndrome (DBS) and facio-oculoacoustico-renal syndrome (FOAR).[provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP2	NM_004525.3	c.12462-850C>T		intron_variant		ENST00000649046.1
LRP2	XM_011511183.4	c.12333-850C>T		intron_variant
LRP2	XM_011511184.3	c.10173-850C>T		intron_variant
LRP2	XM_047444340.1	c.11538-850C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP2	ENST00000649046.1	c.12462-850C>T		intron_variant			NM_004525.3	P1
LRP2	ENST00000649153.1	c.3362-850C>T		intron_variant, NMD_transcript_variant
LRP2	ENST00000650252.1	c.*173-850C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70036 AN: 151780 Hom.: 16825 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.461 AC: 70081 AN: 151898 Hom.: 16838 Cov.: 31 AF XY: 0.461 AC XY: 34199 AN XY: 74218

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.463

Alfa AF: 0.492 Hom.: 2343

Bravo AF: 0.468

Asia WGS AF: 0.346 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.5
Dann	Benign	0.61

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: rs4667593; hg19: chr2-170008386;