dbSNP rs5930: LDLR:p.Arg471Arg (chr19-11113589-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000527.5(LDLR):c.1413A>G(p.Arg471Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 1,613,574 control chromosomes in the GnomAD database, including 313,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 33019 hom., cov: 31)

Exomes 𝑓: 0.62 ( 280017 hom. )

Consequence

LDLR
NM_000527.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:19

Conservation

PhyloP100: -0.476

Publications

103 publications found

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:50121): (microRNA 6886) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR6886 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 19-11113589-A-G is Benign according to our data. Variant chr19-11113589-A-G is described in ClinVar as Benign. ClinVar VariationId is 200916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.476 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000527.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LDLR	NM_000527.5	MANE Select	c.1413A>G	p.Arg471Arg	synonymous	Exon 10 of 18	NP_000518.1	P01130-1
LDLR	NM_001195798.2		c.1413A>G	p.Arg471Arg	synonymous	Exon 10 of 18	NP_001182727.1	P01130-5
LDLR	NM_001195799.2		c.1290A>G	p.Arg430Arg	synonymous	Exon 9 of 17	NP_001182728.1	P01130-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
LDLR	ENST00000558518.6	TSL:1 MANE Select	c.1413A>G	p.Arg471Arg	synonymous	Exon 10 of 18	ENSP00000454071.1	P01130-1
LDLR	ENST00000252444.10	TSL:1	c.1671A>G	p.Arg557Arg	synonymous	Exon 10 of 18	ENSP00000252444.6	J3KMZ9
LDLR	ENST00000558013.5	TSL:1	c.1413A>G	p.Arg471Arg	synonymous	Exon 10 of 18	ENSP00000453346.1	P01130-5

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

99478

AN:

151868

Hom.:

32972

Cov.:

show subpopulations

Gnomad AFR

AF:

0.747

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.694

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.619

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.626

GnomAD2 exomes

AF:

0.632

AC:

158684

AN:

251072

AF XY:

0.626

show subpopulations

Gnomad AFR exome

AF:

0.747

Gnomad AMR exome

AF:

0.712

Gnomad ASJ exome

AF:

0.631

Gnomad EAS exome

AF:

0.609

Gnomad FIN exome

AF:

0.639

Gnomad NFE exome

AF:

0.601

Gnomad OTH exome

AF:

0.612

GnomAD4 exome

AF:

0.618

AC:

902905

AN:

1461586

Hom.:

280017

Cov.:

AF XY:

0.616

AC XY:

448236

AN XY:

727108

show subpopulations

African (AFR)

AF:

0.758

AC:

25373

AN:

33478

American (AMR)

AF:

0.710

AC:

31761

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

16448

AN:

26132

East Asian (EAS)

AF:

0.609

AC:

24157

AN:

39696

South Asian (SAS)

AF:

0.613

AC:

52865

AN:

86250

European-Finnish (FIN)

AF:

0.630

AC:

33621

AN:

53350

Middle Eastern (MID)

AF:

0.610

AC:

3520

AN:

5768

European-Non Finnish (NFE)

AF:

0.610

AC:

677824

AN:

1111806

Other (OTH)

AF:

0.618

AC:

37336

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

20363

40726

61089

81452

101815

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18480

36960

55440

73920

92400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.655

AC:

99574

AN:

151988

Hom.:

33019

Cov.:

AF XY:

0.656

AC XY:

48751

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.747

AC:

31009

AN:

41488

American (AMR)

AF:

0.694

AC:

10593

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.619

AC:

2147

AN:

3470

East Asian (EAS)

AF:

0.610

AC:

3137

AN:

5140

South Asian (SAS)

AF:

0.619

AC:

2978

AN:

4808

European-Finnish (FIN)

AF:

0.647

AC:

6828

AN:

10558

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.602

AC:

40900

AN:

67954

Other (OTH)

AF:

0.624

AC:

1315

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1727

3455

5182

6910

8637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.615

Hom.:

93317

Bravo

AF:

0.663

Asia WGS

AF:

0.582

AC:

2027

AN:

3478

EpiCase

AF:

0.604

EpiControl

AF:

0.608

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Hypercholesterolemia, familial, 1 (7)

not specified (5)

Familial hypercholesterolemia (4)

not provided (2)

Cardiovascular phenotype (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.7

(source)

DANN

Benign

0.54

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over