19-11111644-G-C

Position:

• chr19-11111644-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3 PP4

This summary comes from the ClinGen Evidence Repository: The NM_000527.5 (LDLR):c.1186+5G>C variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PP4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012).The supporting evidence is as follows:PM2: PopMaxMAF = 0.0000809 in African/African American population in gnomAD (gnomAD v2.1.1).The PopMax is African/African American for this variant. However the allele number at this position for 19-11222320-G-C is 2 / 8710, which is < 10,000 in total and only genome data is available. Exome data from a neighboring variant 19-11222323-C-T, allele number 15994, was used for PopMaxMAF calculation:PopMaxMAF = 2 / (15994 + 8710) = 0.0000809 in African/African American populationPP3: Variant is located within canonical intron 8 donor motif, splicing prediction is performed using MES: Wild type canonical donor motif tggGTGAGC score = 7.23, Variant canonical donor motif tggGTGACC score = 0.50, Var Score/Wt Score Ratio = 0.0692 which is <0.8, therefore PP3 is met. Predicted impact for alternative splicing caused by this variant is also confirmed by SpliceAI.PP4: Variant meets PM2 and is identified in 1 index case who fulfil Simon Broome criteria for possible FH and DLCN score = 6 (PMID 32220565, Table 2), after alternative causes of high cholesterol were excluded, reported by Brown et al, 2020, from Johns Hopkins University, US.PS3 not met: Functional data is not available. LINK:https://erepo.genome.network/evrepo/ui/classification/CA16602324/MONDO:0007750/013

• Frequency: Genomes: 𝑓 0.000013 (0 hom., cov: 31)
• Consequence: LDLR NM_000527.5 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Uncertain significance reviewed by expert panel P:2 U:6
• Conservation: PhyloP100: 5.28

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.1186+5G>C		splice_donor_5th_base_variant, intron_variant		ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.1186+5G>C		splice_donor_5th_base_variant, intron_variant		1	NM_000527.5	P3

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152228 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000482

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 32

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152228 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74370

Gnomad4 AFR AF: 0.0000482

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:2 Uncertain:6

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:1 Uncertain:3

Uncertain significance, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	Jan 21, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	Dec 16, 2016	subject mutated among 2600 FH index cases screened = 1 -
Uncertain significance, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Mar 24, 2023	The NM_000527.5 (LDLR):c.1186+5G>C variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PP4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2: PopMaxMAF = 0.0000809 in African/African American population in gnomAD (gnomAD v2.1.1). The PopMax is African/African American for this variant. However the allele number at this position for 19-11222320-G-C is 2 / 8710, which is < 10,000 in total and only genome data is available. Exome data from a neighboring variant 19-11222323-C-T, allele number 15994, was used for PopMaxMAF calculation: PopMaxMAF = 2 / (15994 + 8710) = 0.0000809 in African/African American population PP3: Variant is located within canonical intron 8 donor motif, splicing prediction is performed using MES: Wild type canonical donor motif tggGTGAGC score = 7.23, Variant canonical donor motif tggGTGACC score = 0.50, Var Score/Wt Score Ratio = 0.0692 which is <0.8, therefore PP3 is met. Predicted impact for alternative splicing caused by this variant is also confirmed by SpliceAI. PP4: Variant meets PM2 and is identified in 1 index case who fulfil Simon Broome criteria for possible FH and DLCN score = 6 (PMID 32220565, Table 2), after alternative causes of high cholesterol were excluded, reported by Brown et al, 2020, from Johns Hopkins University, US. PS3 not met: Functional data is not available. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 13, 2023	This variant causes a G to C nucleotide substitution at the +5 position of intron 8 of the LDLR gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. To our knowledge, RNA studies have not been reported for this variant. This variant has been reported in two individuals affected with familial hypercholesterolemia (PMID: 31345425, 32220565). This variant has been identified in 2/31392 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same splice site, c.1186+5G>A, is considered to be disease-causing (ClinVar variation ID: 251706). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2022

Intronic +5 splice site variant in a gene for which loss of function is a known mechanism of disease, and both splice predictors and evolutionary conservation support a deleterious effect; although, in the absence of functional evidence the actual effect of this sequence change is unknown; This variant is associated with the following publications: (PMID: 32220565) -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Feb 20, 2019

Variant summary: LDLR c.1186+5G>C alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a 5' splicing donor site. Three predict the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies (ACMG PP3). The variant allele was found at a frequency of 6.5e-05 in 30960 control chromosomes (gnomAD) indicating that this is a rare allele (ACMG PM2). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1186+5G>C in individuals affected with Familial Hypercholesterolemia (FH) and no experimental evidence demonstrating its impact on protein function have been reported in the literature. However, another variant affecting the same nucleotide, c.1186+5G>A, has been predicted computationally to have similar splicing effect as the variant of interest and confirmed to generate an early stop codon after exon 8 by RT-PCR analysis while, it was functionally determined to affect LDLR expression, LDL binding, and LDL internalization. In addition, c.1186+5G>A was found in multiple FH patients (Etxebarria_2012, PMID 21990180; Amsellem_2002, PMID: 12436241). c.1186+5G>A has not yet been observed in our internal testing experience at the time of this classification. Three more neighboring splicing variants have been reported in the HGMD database as being associated with FH. Two ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as pathogenic (1x) and once as likely pathogenic. One of the submissions describes the detection of the variant in one FH subject. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic, until additional functional or clinical data become available. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 05, 2021

The c.1186+5G>C intronic variant results from a G to C substitution 5 nucleotides after coding exon 8 in the LDLR gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Another alteration impacting the same donor site (c.1186+5G>A) has been described in hypercholesterolemia cohorts, and studies showed RNA splicing and LDLR functional impacts (Amsellem S et al. Hum Genet, 2002 Dec;111:501-10; Etxebarria A et al. Hum Mutat, 2012 Jan;33:232-43). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Familial hypercholesterolemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Aug 04, 2023

Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 375809). This variant has been observed in individual(s) with familial hypercholesterolemia (PMID: 31345425, 32220565). This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change falls in intron 8 of the LDLR gene. It does not directly change the encoded amino acid sequence of the LDLR protein. It affects a nucleotide within the consensus splice site. This variant disrupts the c.1186+5G nucleotide in the LDLR gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 12436241, 18096825, 21990180). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Pathogenic	33
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.93		Position offset: -9
DS_DL_spliceai		0.78		Position offset: -5

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

Publications

LitVar

Other links and lift over

dbSNP: rs879254821; hg19: chr19-11222320;