19-11113505-C-T

Position:

chr19-11113505-C-T

Variant summary

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

The NM_000527.5(LDLR):c.1359-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 1,612,554 control chromosomes in the GnomAD database, including 155,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 11031 hom., cov: 30)

Exomes 𝑓: 0.44 ( 144400 hom. )

Consequence

LDLR
NM_000527.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -0.637

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:

MIR6886 (HGNC:):

MIR6886 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 19-11113505-C-T is Benign according to our data. Variant chr19-11113505-C-T is described in ClinVar as [Benign]. Clinvar id is 251806.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11113505-C-T is described in Lovd as [Likely_benign]. Variant chr19-11113505-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5 linkuse as main transcript	c.1359-30C>T		intron_variant		ENST00000558518.6	NP_000518.1	P01130-1A0A024R7D5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6 linkuse as main transcript	c.1359-30C>T		intron_variant		1	NM_000527.5	ENSP00000454071.1		P01130-1

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

51991

AN:

151818

Hom.:

11044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0908

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.392

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.368

GnomAD3 exomes

AF:

0.398

AC:

99474

AN:

250150

Hom.:

21399

AF XY:

0.405

AC XY:

54798

AN XY:

135338

show subpopulations

Gnomad AFR exome

AF:

0.0825

Gnomad AMR exome

AF:

0.422

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.173

Gnomad SAS exome

AF:

0.388

Gnomad FIN exome

AF:

0.494

Gnomad NFE exome

AF:

0.449

Gnomad OTH exome

AF:

0.420

GnomAD4 exome

AF:

0.437

AC:

638051

AN:

1460618

Hom.:

144400

Cov.:

AF XY:

0.436

AC XY:

317033

AN XY:

726604

show subpopulations

Gnomad4 AFR exome

AF:

0.0754

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.469

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.394

Gnomad4 FIN exome

AF:

0.483

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.417

GnomAD4 genome

AF:

0.342

AC:

51967

AN:

151936

Hom.:

11031

Cov.:

AF XY:

0.346

AC XY:

25688

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.0905

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.456

Gnomad4 EAS

AF:

0.171

Gnomad4 SAS

AF:

0.391

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.451

Gnomad4 OTH

AF:

0.366

Alfa

AF:

0.351

Hom.:

2446

Bravo

AF:

0.325

Asia WGS

AF:

0.267

AC:

929

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1

Benign:6

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
Benign, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Benign, criteria provided, single submitter	research	Iberoamerican FH Network	Mar 01, 2016	- -
Benign, criteria provided, single submitter	research	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	Mar 01, 2016	- -
Benign, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Benign, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

- -

Cardiovascular phenotype

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 17, 2018

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. -

Familial hypercholesterolemia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Mar 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.3

DANN

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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