rs16845213

Positions:

• chr2-141050027-T-C

Variant summary

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

The NM_018557.3(LRP1B):​c.1553-805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,822 control chromosomes in the GnomAD database, including 5,028 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 0.24 (5028 hom., cov: 32)
• Consequence: LRP1B NM_018557.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRP1B	NM_018557.3	c.1553-805A>G		intron_variant		ENST00000389484.8	NP_061027.2
LRP1B	XM_017004341.2	c.1163-805A>G		intron_variant			XP_016859830.1
LRP1B	XM_047444771.1	c.1664-805A>G		intron_variant			XP_047300727.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRP1B	ENST00000389484.8	c.1553-805A>G		intron_variant		1	NM_018557.3	ENSP00000374135.3
LRP1B	ENST00000434794.1	c.206-67751A>G		intron_variant		2		ENSP00000413239.1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36713 AN: 151704 Hom.: 5019 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.242 AC: 36734 AN: 151822 Hom.: 5028 Cov.: 32 AF XY: 0.250 AC XY: 18515 AN XY: 74182

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.247

Alfa AF: 0.254 Hom.: 894

Bravo AF: 0.236

Asia WGS AF: 0.333 AC: 1154 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.61

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: rs16845213; hg19: chr2-141807596;