chr2-169151876-G-A

Variant names:

• chr2-169151876-G-A
• rs4667593
• NM_004525.3:c.12462-850C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

LRP2 Gene-Disease associations (from GenCC):

• Donnai-Barrow syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• Stickler syndrome

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRP2	NM_004525.3	c.12462-850C>T		intron_variant	Intron 67 of 78	ENST00000649046.1	NP_004516.2
LRP2	XM_011511183.4	c.12333-850C>T		intron_variant	Intron 66 of 77		XP_011509485.1
LRP2	XM_047444340.1	c.11538-850C>T		intron_variant	Intron 67 of 78		XP_047300296.1
LRP2	XM_011511184.3	c.10173-850C>T		intron_variant	Intron 52 of 63		XP_011509486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP2	ENST00000649046.1	c.12462-850C>T		intron_variant	Intron 67 of 78		NM_004525.3	ENSP00000496870.1
LRP2	ENST00000649153.1	n.3360-850C>T		intron_variant	Intron 19 of 29			ENSP00000497617.1
LRP2	ENST00000650252.1	n.*173-850C>T		intron_variant	Intron 12 of 23			ENSP00000496887.1

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

African (AFR) AF: 0.389 AC: 16131 AN: 41416

American (AMR) AF: 0.596 AC: 9110 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1538 AN: 3466

East Asian (EAS) AF: 0.100 AC: 517 AN: 5164

South Asian (SAS) AF: 0.469 AC: 2251 AN: 4802

European-Finnish (FIN) AF: 0.449 AC: 4719 AN: 10518

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34289 AN: 67934

Other (OTH) AF: 0.463 AC: 977 AN: 2108

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
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4667593; hg19: chr2-170008386;