NM_002336.3:c.449+9169A>T

Variant names:

• chr12-12235093-T-A
• rs11054738
• NM_002336.3:c.449+9169A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002336.3(LRP6):​c.449+9169A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,132 control chromosomes in the GnomAD database, including 1,895 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 0.15 (1895 hom., cov: 32)
• Consequence: LRP6 NM_002336.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 6 publications found

Genes affected

LRP6 (HGNC:6698): (LDL receptor related protein 6) This gene encodes a member of the low density lipoprotein (LDL) receptor gene family. LDL receptors are transmembrane cell surface proteins involved in receptor-mediated endocytosis of lipoprotein and protein ligands. The protein encoded by this gene functions as a receptor or, with Frizzled, a co-receptor for Wnt and thereby transmits the canonical Wnt/beta-catenin signaling cascade. Through its interaction with the Wnt/beta-catenin signaling cascade this gene plays a role in the regulation of cell differentiation, proliferation, and migration and the development of many cancer types. This protein undergoes gamma-secretase dependent RIP- (regulated intramembrane proteolysis) processing but the precise locations of the cleavage sites have not been determined.[provided by RefSeq, Dec 2009]

LRP6 Gene-Disease associations (from GenCC):

• tooth agenesis

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
• tooth agenesis, selective, 7

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
• coronary artery disease, autosomal dominant 2

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002336.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRP6	NM_002336.3	MANE Select	c.449+9169A>T		intron	N/A	NP_002327.2
	LRP6	NM_001414244.1		c.449+9169A>T		intron	N/A	NP_001401173.1
	LRP6	NM_001414245.1		c.449+9169A>T		intron	N/A	NP_001401174.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRP6	ENST00000261349.9	TSL:1 MANE Select	c.449+9169A>T		intron	N/A	ENSP00000261349.4
	LRP6	ENST00000543091.1	TSL:1	c.449+9169A>T		intron	N/A	ENSP00000442472.1
	LRP6	ENST00000538239.5	TSL:1	n.41+9169A>T		intron	N/A	ENSP00000445083.1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22684 AN: 152012 Hom.: 1895 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.149 AC: 22695 AN: 152132 Hom.: 1895 Cov.: 32 AF XY: 0.146 AC XY: 10889 AN XY: 74374

African (AFR) AF: 0.0993 AC: 4121 AN: 41508

American (AMR) AF: 0.114 AC: 1747 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3472

East Asian (EAS) AF: 0.0506 AC: 262 AN: 5180

South Asian (SAS) AF: 0.105 AC: 504 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2015 AN: 10562

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12916 AN: 67978

Other (OTH) AF: 0.142 AC: 299 AN: 2112

Alfa AF: 0.102 Hom.: 159

Bravo AF: 0.141

Asia WGS AF: 0.0870 AC: 303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.72
PhyloP100		0.38
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: rs11054738; hg19: chr12-12388027;