chr2-142044372-T-C

Position:

• chr2-142044372-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018557.3(LRP1B):​c.82+86276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,412 control chromosomes in the GnomAD database, including 22,434 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 0.54 (22434 hom., cov: 31)
• Consequence: LRP1B NM_018557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP1B	NM_018557.3	c.82+86276A>G		intron_variant		ENST00000389484.8
LRP1B	XM_017004341.2	c.-309+64488A>G		intron_variant
LRP1B	XM_047444771.1	c.193+86276A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP1B	ENST00000389484.8	c.82+86276A>G		intron_variant		1	NM_018557.3	P1
LRP1B	ENST00000434794.1	c.82+86276A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81037 AN: 151294 Hom.: 22416 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.536 AC: 81085 AN: 151412 Hom.: 22434 Cov.: 31 AF XY: 0.539 AC XY: 39889 AN XY: 73958

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.531

Alfa AF: 0.562 Hom.: 13734

Bravo AF: 0.530

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.38		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.38		Position offset: -45

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2029142; hg19: chr2-142801941;