chr2-142050747-G-C

Position:

• chr2-142050747-G-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+79901C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,838 control chromosomes in the GnomAD database, including 16,038 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 0.43 (16038 hom., cov: 32)
• Consequence: LRP1B NM_018557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP1B	NM_018557.3	c.82+79901C>G		intron_variant		ENST00000389484.8
LRP1B	XM_017004341.2	c.-309+58113C>G		intron_variant
LRP1B	XM_047444771.1	c.193+79901C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP1B	ENST00000389484.8	c.82+79901C>G		intron_variant		1	NM_018557.3	P1
LRP1B	ENST00000434794.1	c.82+79901C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65488 AN: 151720 Hom.: 16033 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.431 AC: 65485 AN: 151838 Hom.: 16038 Cov.: 32 AF XY: 0.435 AC XY: 32283 AN XY: 74164

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.444

Alfa AF: 0.343 Hom.: 1016

Bravo AF: 0.427

Asia WGS AF: 0.470 AC: 1631 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.46

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: rs1449504; hg19: chr2-142808316;