rs10496915

chr2-142125024-A-C

Variant summary

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

The NM_018557.3(LRP1B):c.82+5624T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,580 control chromosomes in the GnomAD database, including 5,791 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 0.25 (5791 hom., cov: 32)
• Consequence: LRP1B NM_018557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

LRP1B (HGNC:6693): (LDL receptor related protein 1B) This gene encodes a member of the low density lipoprotein (LDL) receptor family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands. Disruption of this gene has been reported in several types of cancer. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP1B	NM_018557.3	c.82+5624T>G		intron_variant		ENST00000389484.8
LRP1B	XM_047444771.1	c.193+5624T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP1B	ENST00000389484.8	c.82+5624T>G		intron_variant		1	NM_018557.3	P1
LRP1B	ENST00000434794.1	c.82+5624T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37230 AN: 151462 Hom.: 5775 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.246 AC: 37285 AN: 151580 Hom.: 5791 Cov.: 32 AF XY: 0.245 AC XY: 18177 AN XY: 74080

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.247

Alfa AF: 0.177 Hom.: 5486

Bravo AF: 0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.7
Dann	Benign	0.77

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: rs10496915; hg19: chr2-142882593;