rs2788032

Variant names:

• chr1-53311959-A-C
• rs2788032
• NM_004631.5:c.244+14914T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-53311959-A-C
• chr1-53311959-A-G
• chr1-53311959-A-T

Variant summary

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

The NM_004631.5(LRP8):​c.244+14914T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,142 control chromosomes in the GnomAD database, including 2,570 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 0.16 (2570 hom., cov: 33)
• Consequence: LRP8 NM_004631.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 5 publications found

Genes affected

LRP8 (HGNC:6700): (LDL receptor related protein 8) This gene encodes a member of the low density lipoprotein receptor (LDLR) family. Low density lipoprotein receptors are cell surface proteins that play roles in both signal transduction and receptor-mediated endocytosis of specific ligands for lysosomal degradation. The encoded protein plays a critical role in the migration of neurons during development by mediating Reelin signaling, and also functions as a receptor for the cholesterol transport protein apolipoprotein E. Expression of this gene may be a marker for major depressive disorder. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jun 2011]

LRP8 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP8	NM_004631.5	c.244+14914T>G		intron_variant	Intron 2 of 18	ENST00000306052.12	NP_004622.2
LRP8	NM_001018054.3	c.244+14914T>G		intron_variant	Intron 2 of 17		NP_001018064.1
LRP8	NM_033300.4	c.244+14914T>G		intron_variant	Intron 2 of 16		NP_150643.2
LRP8	NM_017522.5	c.244+14914T>G		intron_variant	Intron 2 of 15		NP_059992.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP8	ENST00000306052.12	c.244+14914T>G		intron_variant	Intron 2 of 18	1	NM_004631.5	ENSP00000303634.6

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23648 AN: 152024 Hom.: 2561 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.156 AC: 23699 AN: 152142 Hom.: 2570 Cov.: 33 AF XY: 0.155 AC XY: 11556 AN XY: 74362

African (AFR) AF: 0.314 AC: 13020 AN: 41488

American (AMR) AF: 0.0750 AC: 1146 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.0625 AC: 323 AN: 5172

South Asian (SAS) AF: 0.201 AC: 969 AN: 4816

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10592

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6492 AN: 68000

Other (OTH) AF: 0.128 AC: 271 AN: 2112

Alfa AF: 0.113 Hom.: 1572

Bravo AF: 0.158

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-1.1
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: rs2788032; hg19: chr1-53777631; COSMIC: COSV60097130; COSMIC: COSV60097130;