rs4245855

chr2-141391759-G-A

Variant summary

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

The NM_018557.3(LRP1B):c.343+88637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,008 control chromosomes in the GnomAD database, including 24,702 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 0.55 (24702 hom., cov: 32)
• Consequence: LRP1B NM_018557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP1B	NM_018557.3	c.343+88637C>T		intron_variant		ENST00000389484.8
LRP1B	XM_017004341.2	c.-48+88637C>T		intron_variant
LRP1B	XM_047444771.1	c.454+88637C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP1B	ENST00000389484.8	c.343+88637C>T		intron_variant		1	NM_018557.3	P1
LRP1B	ENST00000434794.1	c.206-409483C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83926 AN: 151890 Hom.: 24697 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.552 AC: 83960 AN: 152008 Hom.: 24702 Cov.: 32 AF XY: 0.549 AC XY: 40802 AN XY: 74312

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.565

Alfa AF: 0.635 Hom.: 53385

Bravo AF: 0.528

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.084
Dann	Benign	0.45

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: rs4245855; hg19: chr2-142149328;