Variant chr12-57197443-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002332.3(LRP1):c.9162+59T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,609,872 control chromosomes in the GnomAD database, including 97,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14926 hom., cov: 32)

Exomes 𝑓: 0.33 ( 82644 hom. )

Consequence

LRP1
NM_002332.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.75

Variant links:

Genes affected

LRP1 (HGNC:6692): (LDL receptor related protein 1) This gene encodes a member of the low-density lipoprotein receptor family of proteins. The encoded preproprotein is proteolytically processed by furin to generate 515 kDa and 85 kDa subunits that form the mature receptor (PMID: 8546712). This receptor is involved in several cellular processes, including intracellular signaling, lipid homeostasis, and clearance of apoptotic cells. In addition, the encoded protein is necessary for the alpha 2-macroglobulin-mediated clearance of secreted amyloid precursor protein and beta-amyloid, the main component of amyloid plaques found in Alzheimer patients. Expression of this gene decreases with age and has been found to be lower than controls in brain tissue from Alzheimer's disease patients. [provided by RefSeq, Oct 2015]

LRP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 12-57197443-T-C is Benign according to our data. Variant chr12-57197443-T-C is described in ClinVar as [Benign]. Clinvar id is 1267665.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRP1	NM_002332.3 linkuse as main transcript	c.9162+59T>C		intron_variant		ENST00000243077.8	NP_002323.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRP1	ENST00000243077.8 linkuse as main transcript	c.9162+59T>C		intron_variant		1	NM_002332.3	ENSP00000243077	P1	Q07954-1

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63714

AN:

151812

Hom.:

14889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.430

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.394

GnomAD4 exome

AF:

0.328

AC:

477813

AN:

1457942

Hom.:

82644

Cov.:

AF XY:

0.321

AC XY:

233063

AN XY:

725336

show subpopulations

Gnomad4 AFR exome

AF:

0.637

Gnomad4 AMR exome

AF:

0.512

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.409

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.399

Gnomad4 NFE exome

AF:

0.313

Gnomad4 OTH exome

AF:

0.340

GnomAD4 genome

AF:

0.420

AC:

63805

AN:

151930

Hom.:

14926

Cov.:

AF XY:

0.418

AC XY:

31002

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.629

Gnomad4 AMR

AF:

0.409

Gnomad4 ASJ

AF:

0.322

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.315

Gnomad4 OTH

AF:

0.393

Alfa

AF:

0.249

Hom.:

766

Bravo

AF:

0.441

Asia WGS

AF:

0.419

AC:

1457

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.2

DANN

Benign

0.16

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over