rs10496915

Variant names:

• chr2-142125024-A-C
• rs10496915
• NM_018557.3:c.82+5624T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRP1B	NM_018557.3	c.82+5624T>G		intron_variant	Intron 1 of 90	ENST00000389484.8	NP_061027.2
LRP1B	XM_047444771.1	c.193+5624T>G		intron_variant	Intron 1 of 76		XP_047300727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP1B	ENST00000389484.8	c.82+5624T>G		intron_variant	Intron 1 of 90	1	NM_018557.3	ENSP00000374135.3
LRP1B	ENST00000434794.1	c.82+5624T>G		intron_variant	Intron 1 of 13	2		ENSP00000413239.1

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

African (AFR) AF: 0.437 AC: 18079 AN: 41378

American (AMR) AF: 0.276 AC: 4201 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3468

East Asian (EAS) AF: 0.175 AC: 903 AN: 5152

South Asian (SAS) AF: 0.196 AC: 948 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1095 AN: 10582

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10689 AN: 67658

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.194 Hom.: 11543

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
PhyloP100		-0.12
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: rs10496915; hg19: chr2-142882593;