rs1799898

Positions:

chr19-11116878-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000527.5(LDLR):c.1725C>T(p.Leu575=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,613,742 control chromosomes in the GnomAD database, including 13,006 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 994 hom., cov: 32)

Exomes 𝑓: 0.12 ( 12012 hom. )

Consequence

LDLR
NM_000527.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:18

Conservation

PhyloP100: -0.878

Variant links:

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

LDLR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 19-11116878-C-T is Benign according to our data. Variant chr19-11116878-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 251997.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11116878-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.878 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5 linkuse as main transcript	c.1725C>T	p.Leu575=	synonymous_variant	12/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6 linkuse as main transcript	c.1725C>T	p.Leu575=	synonymous_variant	12/18	1	NM_000527.5	P3	P01130-1

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16752

AN:

152056

Hom.:

991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.0866

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.00752

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.112

AC:

28272

AN:

251468

Hom.:

1799

AF XY:

0.117

AC XY:

15840

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0821

Gnomad AMR exome

AF:

0.0702

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.00680

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.130

GnomAD4 exome

AF:

0.124

AC:

181747

AN:

1461568

Hom.:

12012

Cov.:

AF XY:

0.125

AC XY:

91118

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.0811

Gnomad4 AMR exome

AF:

0.0715

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.00662

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.131

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.110

AC:

16766

AN:

152174

Hom.:

994

Cov.:

AF XY:

0.110

AC XY:

8200

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0820

Gnomad4 AMR

AF:

0.0864

Gnomad4 ASJ

AF:

0.151

Gnomad4 EAS

AF:

0.00773

Gnomad4 SAS

AF:

0.127

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.127

Hom.:

1096

Bravo

AF:

0.105

Asia WGS

AF:

0.0910

AC:

317

AN:

3478

EpiCase

AF:

0.140

EpiControl

AF:

0.140

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:18

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1

Benign:7

Benign, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	4 Hmz + 27 Htz / 125 non-FH individuals; MAF = 11,0% in 86 Spanish healthy individuals -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 22, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen	Jun 11, 2018	Due to the increased occurrence of the mutation (>= 5%), this variant is classified as benign. -
Benign, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -

not specified

Benign:5

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 15, 2017	Leu575Leu in exon 12 of LDLR: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 13.8% (1072/8600) of European chromosomes from a broad population by the Exome Aggregation Consortiu m (ExAC, http://exac.broadinstitute.org; dbSNP rs1799898). -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Familial hypercholesterolemia

Benign:4

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, no assertion criteria provided	clinical testing	Cohesion Phenomics	Feb 09, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GENinCode PLC	Jul 14, 2022	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Cardiovascular phenotype

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 23, 2016

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

4.1

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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